7Q7J

Room temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at 75 MPa helium gas pressure in a sapphire capillary

PDB DOI: https://doi.org/10.2210/pdb7Q7J/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2021-11-09 Released: 2022-11-16
Deposition Author(s): Lieske, J., Guenther, S., Saouane, S., Selikhanov, G.K., Gabdulkhakov, A.G., Meents, A.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.231
R-Value Work: 0.179
R-Value Observed: 0.181

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fixed-target high-pressure macromolecular crystallography

Lieske, J., Saouane, S., Guenther, S., Meyer, J., Pakendorf, T., Reime, B., Burkhardt, A., Crosas, E., Hakanpaeae, J., Stachnik, K., Sieg, J., Rarey, M., Abdellatif, M.H., Gabdulkhakov, A.G., Selikhanov, G.K., Chapman, H.N., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 101.34 kDa
Atom Count: 7,390
Modelled Residue Count: 821
Deposited Residue Count: 824
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	A [auth H]	241	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	281	Cereibacter sphaeroides	Mutation(s): 1 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	302	Cereibacter sphaeroides	Mutation(s): 2 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain N [auth M] SDF format, chain O [auth M] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain N [auth M] MOL2 format, chain O [auth M] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain N [auth M] mmCIF format, chain O [auth M]	G [auth L], H [auth L], N [auth M], O [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain N [auth M] Focus chain O [auth M] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain N [auth M] Focus chain O [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain L [auth M] MOL2 format, chain F [auth L] MOL2 format, chain L [auth M] mmCIF format, chain F [auth L] mmCIF format, chain L [auth M]	F [auth L], L [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain F [auth L] Focus chain L [auth M] Interactions & Density Focus chain F [auth L] Focus chain L [auth M]
UQ7 (Subject of Investigation/LOI) Query on UQ7 Download Ideal Coordinates CCD File SDF format, chain M MOL2 format, chain M mmCIF format, chain M	M	UBIQUINONE-7 C₄₄ H₆₆ O₄ DBESHHFMIFSNRV-RJYQSXAYSA-N		Interactions Focus chain M Interactions & Density Focus chain M
SPN (Subject of Investigation/LOI) Query on SPN Download Ideal Coordinates CCD File SDF format, chain U [auth M] MOL2 format, chain U [auth M] mmCIF format, chain U [auth M]	U [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain U [auth M] Interactions & Density Focus chain U [auth M]
OLC (Subject of Investigation/LOI) Query on OLC Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain T [auth M] MOL2 format, chain I [auth L] MOL2 format, chain T [auth M] mmCIF format, chain I [auth L] mmCIF format, chain T [auth M]	I [auth L], T [auth M]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain I [auth L] Focus chain T [auth M] Interactions & Density Focus chain I [auth L] Focus chain T [auth M]
LDA (Subject of Investigation/LOI) Query on LDA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain V [auth M] SDF format, chain W [auth M] SDF format, chain X [auth M] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain V [auth M] MOL2 format, chain W [auth M] MOL2 format, chain X [auth M] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain V [auth M] mmCIF format, chain W [auth M] mmCIF format, chain X [auth M]	D [auth H] E [auth H] J [auth L] K [auth L] Q [auth M] D [auth H], E [auth H], J [auth L], K [auth L], Q [auth M], R [auth M], V [auth M], W [auth M], X [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H] Focus chain J [auth L] Focus chain K [auth L] Focus chain Q [auth M] Focus chain R [auth M] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M] Interactions & Density Focus chain D [auth H] Focus chain E [auth H] Focus chain J [auth L] Focus chain K [auth L] Focus chain Q [auth M] Focus chain R [auth M] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain Z [auth M] MOL2 format, chain Z [auth M] mmCIF format, chain Z [auth M]	Z [auth M]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain Z [auth M] Interactions & Density Focus chain Z [auth M]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain S [auth M] SDF format, chain Y [auth M] MOL2 format, chain S [auth M] MOL2 format, chain Y [auth M] mmCIF format, chain S [auth M] mmCIF format, chain Y [auth M]	S [auth M], Y [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain S [auth M] Focus chain Y [auth M] Interactions & Density Focus chain S [auth M] Focus chain Y [auth M]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain P [auth M] MOL2 format, chain P [auth M] mmCIF format, chain P [auth M]	P [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain P [auth M] Interactions & Density Focus chain P [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth M] MOL2 format, chain AA [auth M] mmCIF format, chain AA [auth M]	AA [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth M] Interactions & Density Focus chain AA [auth M]