3LXV | pdb_00003lxv

Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

PDB DOI: https://doi.org/10.2210/pdb3LXV/pdb

Classification: oxidoreductase/oxidoreductase
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-02-25 Released: 2011-03-09
Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.246 (Depositor), 0.260 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

Purpero, V.M., Valley, M.P., Ohlendorf, D.H., Lipscomb, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 150.52 kDa
Atom Count: 11,718
Modelled Residue Count: 1,314
Deposited Residue Count: 1,314
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase alpha chain	A, C [auth B], E [auth C]	200	Pseudomonas putida	Mutation(s): 0 Gene Names: pcaG EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida) Explore P00436 Go to UniProtKB: P00436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00436
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase beta chain	B [auth M], D [auth N], F [auth O]	238	Pseudomonas putida	Mutation(s): 1 Gene Names: pcaH EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida) Explore P00437 Go to UniProtKB: P00437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00437
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4NC Query on 4NC Download Ideal Coordinates CCD File SDF format, chain FA [auth N] SDF format, chain U [auth M] SDF format, chain UA [auth O] SDF format, chain WA [auth O] MOL2 format, chain FA [auth N] MOL2 format, chain U [auth M] MOL2 format, chain UA [auth O] MOL2 format, chain WA [auth O] mmCIF format, chain FA [auth N] mmCIF format, chain U [auth M] mmCIF format, chain UA [auth O] mmCIF format, chain WA [auth O]	FA [auth N], U [auth M], UA [auth O], WA [auth O]	4-NITROCATECHOL C₆ H₅ N O₄ XJNPNXSISMKQEX-UHFFFAOYSA-N		Interactions Focus chain FA [auth N] Focus chain U [auth M] Focus chain UA [auth O] Focus chain WA [auth O] Interactions & Density Focus chain FA [auth N] Focus chain U [auth M] Focus chain UA [auth O] Focus chain WA [auth O]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain SA [auth O] SDF format, chain X [auth B] MOL2 format, chain K [auth A] MOL2 format, chain SA [auth O] MOL2 format, chain X [auth B] mmCIF format, chain K [auth A] mmCIF format, chain SA [auth O] mmCIF format, chain X [auth B]	K [auth A], SA [auth O], X [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Focus chain SA [auth O] Focus chain X [auth B] Interactions & Density Focus chain K [auth A] Focus chain SA [auth O] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain IA [auth C] SDF format, chain V [auth B] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain V [auth B] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain V [auth B]	G [auth A], IA [auth C], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain IA [auth C] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain IA [auth C] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain BA [auth N] SDF format, chain H [auth A] SDF format, chain JA [auth C] SDF format, chain N [auth M] SDF format, chain O [auth M] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain N [auth M] MOL2 format, chain O [auth M] MOL2 format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain BA [auth N] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain N [auth M] mmCIF format, chain O [auth M] mmCIF format, chain Z [auth N]	AA [auth N] BA [auth N] H [auth A] JA [auth C] N [auth M] AA [auth N], BA [auth N], H [auth A], JA [auth C], N [auth M], O [auth M], Z [auth N]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain BA [auth N] Focus chain H [auth A] Focus chain JA [auth C] Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth N] Focus chain H [auth A] Focus chain JA [auth C] Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth N]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain CA [auth N] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain NA [auth O] SDF format, chain OA [auth O] SDF format, chain P [auth M] SDF format, chain PA [auth O] SDF format, chain Q [auth M] SDF format, chain QA [auth O] SDF format, chain R [auth M] SDF format, chain RA [auth O] SDF format, chain W [auth B] SDF format, chain EA [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain NA [auth O] MOL2 format, chain OA [auth O] MOL2 format, chain P [auth M] MOL2 format, chain PA [auth O] MOL2 format, chain Q [auth M] MOL2 format, chain QA [auth O] MOL2 format, chain R [auth M] MOL2 format, chain RA [auth O] MOL2 format, chain W [auth B] MOL2 format, chain EA [auth N] mmCIF format, chain CA [auth N] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain NA [auth O] mmCIF format, chain OA [auth O] mmCIF format, chain P [auth M] mmCIF format, chain PA [auth O] mmCIF format, chain Q [auth M] mmCIF format, chain QA [auth O] mmCIF format, chain R [auth M] mmCIF format, chain RA [auth O] mmCIF format, chain W [auth B] mmCIF format, chain EA [auth N]	CA [auth N] EA [auth N] I [auth A] J [auth A] KA [auth C] CA [auth N], EA [auth N], I [auth A], J [auth A], KA [auth C], LA [auth C], NA [auth O], OA [auth O], P [auth M], PA [auth O], Q [auth M], QA [auth O], R [auth M], RA [auth O], W [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain CA [auth N] Focus chain EA [auth N] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth O] Focus chain OA [auth O] Focus chain P [auth M] Focus chain PA [auth O] Focus chain Q [auth M] Focus chain QA [auth O] Focus chain R [auth M] Focus chain RA [auth O] Focus chain W [auth B] Interactions & Density Focus chain CA [auth N] Focus chain EA [auth N] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth O] Focus chain OA [auth O] Focus chain P [auth M] Focus chain PA [auth O] Focus chain Q [auth M] Focus chain QA [auth O] Focus chain R [auth M] Focus chain RA [auth O] Focus chain W [auth B]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain GA [auth N] SDF format, chain L [auth A] SDF format, chain MA [auth C] SDF format, chain S [auth M] SDF format, chain T [auth M] MOL2 format, chain GA [auth N] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] mmCIF format, chain GA [auth N] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M]	GA [auth N], L [auth A], MA [auth C], S [auth M], T [auth M]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain GA [auth N] Focus chain L [auth A] Focus chain MA [auth C] Focus chain S [auth M] Focus chain T [auth M] Interactions & Density Focus chain GA [auth N] Focus chain L [auth A] Focus chain MA [auth C] Focus chain S [auth M] Focus chain T [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain DA [auth N] SDF format, chain M SDF format, chain VA [auth O] MOL2 format, chain DA [auth N] MOL2 format, chain M MOL2 format, chain VA [auth O] mmCIF format, chain DA [auth N] mmCIF format, chain M mmCIF format, chain VA [auth O]	DA [auth N], M, VA [auth O]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DA [auth N] Focus chain M Focus chain VA [auth O] Interactions & Density Focus chain DA [auth N] Focus chain M Focus chain VA [auth O]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth N] SDF format, chain TA [auth O] SDF format, chain Y [auth B] MOL2 format, chain HA [auth N] MOL2 format, chain TA [auth O] MOL2 format, chain Y [auth B] mmCIF format, chain HA [auth N] mmCIF format, chain TA [auth O] mmCIF format, chain Y [auth B]	HA [auth N], TA [auth O], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth N] Focus chain TA [auth O] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth N] Focus chain TA [auth O] Focus chain Y [auth B]