7B9A | pdb_00007b9a

CooS-V with Xe-soaked

PDB DOI: https://doi.org/10.2210/pdb7B9A/pdb

Classification: OXIDOREDUCTASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-14 Released: 2022-01-12
Deposition Author(s): Jeoung, J.H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.276 (Depositor), 0.280 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold.

Jeoung, J.H., Fesseler, J., Domnik, L., Klemke, F., Sinnreich, M., Teutloff, C., Dobbek, H.

(2022) Angew Chem Int Ed Engl 61: e202117000-e202117000

PubMed: 35133707 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.202117000
Primary Citation of Related Structures:
7B7Q, 7B7T, 7B95, 7B97, 7B9A

PubMed Abstract:
Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO ₂ to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-V _Ch . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-V _Ch catalyzes neither CO oxidation, nor CO ₂ reduction. The active site of CooS-V _Ch undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H ₂ O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-V _Ch , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.

Organizational Affiliation

Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 286.14 kDa
Atom Count: 19,287
Modelled Residue Count: 2,515
Deposited Residue Count: 2,516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	A, B, C, D	629	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: cooSV, CHY_0034 EC: 1.2.7.4
UniProt
Find proteins for Q3AG28 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3AG28 Go to UniProtKB: Q3AG28
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3AG28
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain FC [auth D] MOL2 format, chain E [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain FC [auth D] mmCIF format, chain E [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain FC [auth D]	CB [auth C], DA [auth B], E [auth A], FC [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CB [auth C] Focus chain DA [auth B] Focus chain E [auth A] Focus chain FC [auth D] Interactions & Density Focus chain CB [auth C] Focus chain DA [auth B] Focus chain E [auth A] Focus chain FC [auth D]
T2N (Subject of Investigation/LOI) Query on T2N Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain RB [auth C] SDF format, chain VC [auth D] SDF format, chain X [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain VC [auth D] MOL2 format, chain X [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain VC [auth D] mmCIF format, chain X [auth A]	AB [auth B], RB [auth C], VC [auth D], X [auth A]	3,5-dioxa-7-thia-1-thionia-2$l^{2},4$l^{2},6$l^{3},8$l^{2}-tetraferrabicyclo[4.2.0]octane Fe₄ O₂ S₂ ZZXANUDJVNRRAL-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain RB [auth C] Focus chain VC [auth D] Focus chain X [auth A] Interactions & Density Focus chain AB [auth B] Focus chain RB [auth C] Focus chain VC [auth D] Focus chain X [auth A]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain ZB [auth D] SDF format, chain CA [auth B] MOL2 format, chain ZB [auth D] MOL2 format, chain CA [auth B] mmCIF format, chain ZB [auth D] mmCIF format, chain CA [auth B]	CA [auth B], ZB [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain ZB [auth D] Interactions & Density Focus chain CA [auth B] Focus chain ZB [auth D]
XE (Subject of Investigation/LOI) Query on XE Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BB [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain HC [auth D] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain IC [auth D] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain KC [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain MC [auth D] SDF format, chain N [auth A] SDF format, chain NB [auth C] SDF format, chain NC [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain OC [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain PC [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain QC [auth D] SDF format, chain S [auth A] SDF format, chain SC [auth D] SDF format, chain T [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain GB [auth C] SDF format, chain GC [auth D] SDF format, chain H [auth A] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JC [auth D] SDF format, chain LC [auth D] SDF format, chain NA [auth B] SDF format, chain R [auth A] SDF format, chain RC [auth D] SDF format, chain TC [auth D] SDF format, chain UC [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain HC [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain OC [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SC [auth D] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JC [auth D] MOL2 format, chain LC [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RC [auth D] MOL2 format, chain TC [auth D] MOL2 format, chain UC [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain HC [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain IC [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain NC [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain OC [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain PC [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain QC [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SC [auth D] mmCIF format, chain T [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain GC [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JC [auth D] mmCIF format, chain LC [auth D] mmCIF format, chain NA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RC [auth D] mmCIF format, chain TC [auth D] mmCIF format, chain UC [auth D]	AA [auth A] BB [auth B] DB [auth C] EA [auth B] EB [auth C] AA [auth A], BB [auth B], DB [auth C], EA [auth B], EB [auth C], F [auth A], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], GC [auth D], H [auth A], HA [auth B], HB [auth C], HC [auth D], I [auth A], IA [auth B], IB [auth C], IC [auth D], J [auth A], JA [auth B], JB [auth C], JC [auth D], K [auth A], KA [auth B], KB [auth C], KC [auth D], L [auth A], LA [auth B], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RC [auth D], S [auth A], SC [auth D], T [auth A], TC [auth D], UC [auth D], Y [auth A], Z [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BB [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TC [auth D] Focus chain UC [auth D] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BB [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TC [auth D] Focus chain UC [auth D] Focus chain Y [auth A] Focus chain Z [auth A]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain BC [auth D] SDF format, chain CC [auth D] SDF format, chain DC [auth D] SDF format, chain EC [auth D] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain V [auth A] SDF format, chain VB [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain XB [auth C] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain SB [auth C] SDF format, chain TB [auth C] SDF format, chain VA [auth B] SDF format, chain XA [auth B] MOL2 format, chain AC [auth D] MOL2 format, chain BC [auth D] MOL2 format, chain CC [auth D] MOL2 format, chain DC [auth D] MOL2 format, chain EC [auth D] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth C] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain TB [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain XA [auth B] mmCIF format, chain AC [auth D] mmCIF format, chain BC [auth D] mmCIF format, chain CC [auth D] mmCIF format, chain DC [auth D] mmCIF format, chain EC [auth D] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth C] mmCIF format, chain XB [auth C] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain TB [auth C] mmCIF format, chain VA [auth B] mmCIF format, chain XA [auth B]	AC [auth D] BC [auth D] CC [auth D] DC [auth D] EC [auth D] AC [auth D], BC [auth D], CC [auth D], DC [auth D], EC [auth D], RA [auth B], SA [auth B], SB [auth C], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], V [auth A], VA [auth B], VB [auth C], W [auth A], WA [auth B], WB [auth C], XA [auth B], XB [auth C], YA [auth B], ZA [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain AC [auth D] Focus chain BC [auth D] Focus chain CC [auth D] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AC [auth D] Focus chain BC [auth D] Focus chain CC [auth D] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YA [auth B] Focus chain ZA [auth B]
H2S (Subject of Investigation/LOI) Query on H2S Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain WC [auth D] SDF format, chain YB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain WC [auth D] MOL2 format, chain YB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain WC [auth D] mmCIF format, chain YB [auth C]	BA [auth A], WC [auth D], YB [auth C]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain WC [auth D] Focus chain YB [auth C] Interactions & Density Focus chain BA [auth A] Focus chain WC [auth D] Focus chain YB [auth C]