8VTM

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-bromophenylalanine

PDB DOI: https://doi.org/10.2210/pdb8VTM/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): No

Deposited: 2024-01-26 Released: 2024-03-13
Deposition Author(s): Tran, K., Mathews, I., Boxer, S.G.
Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.261
R-Value Work: 0.220
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-bromophenylalanine

Tran, K., Mathews, I., Boxer, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 99.38 kDa
Atom Count: 6,994
Modelled Residue Count: 822
Deposited Residue Count: 822
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]	240	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: puhA
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): 0 Gene Names: pufL
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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	301	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: pufM
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain N [auth M] MOL2 format, chain N [auth M]	N [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain H [auth M] SDF format, chain P [auth M] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain H [auth M] MOL2 format, chain P [auth M]	E [auth L], F [auth L], H [auth M], P [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain H [auth M] Focus chain P [auth M] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain H [auth M] Focus chain P [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain L [auth M] SDF format, chain O [auth M] MOL2 format, chain L [auth M] MOL2 format, chain O [auth M]	L [auth M], O [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain L [auth M] Focus chain O [auth M] Interactions & Density Focus chain L [auth M] Focus chain O [auth M]
SPO Query on SPO Download Ideal Coordinates CCD File SDF format, chain M MOL2 format, chain M	M	SPHEROIDENE C₄₁ H₆₀ O FJOCMTHZSURUFA-KXCOHNEYSA-N		Interactions Focus chain M Interactions & Density Focus chain M
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain I [auth M] SDF format, chain J [auth M] MOL2 format, chain D [auth H] MOL2 format, chain I [auth M] MOL2 format, chain J [auth M]	D [auth H], I [auth M], J [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain I [auth M] Focus chain J [auth M] Interactions & Density Focus chain D [auth H] Focus chain I [auth M] Focus chain J [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain K [auth M] MOL2 format, chain K [auth M]	K [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain K [auth M] Interactions & Density Focus chain K [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L]	G [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]