7MHA | pdb_00007mha

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant; W252V mutant

PDB DOI: https://doi.org/10.2210/pdb7MHA/pdb

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

Deposited: 2021-04-14 Released: 2022-04-27
Deposition Author(s): Boxer, S.G., Mathews, I.I., Weaver, J.B.
Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.178 (Depositor), 0.185 (DCC)
R-Value Work:
0.156 (Depositor), 0.164 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Photosynthetic reaction center variants made via genetic code expansion indicate tyrosine at M210 tunes the mechanism for primary electron transfer

Weaver, J.B., Lin, C.Y., Faries, K.M., Mathews, I.I., Russi, S., Holten, D., Kirmaier, C., Boxer, S.G.

(2022) Thesis : 294-294

Macromolecule Content

Total Structure Weight: 103.94 kDa
Atom Count: 7,178
Modeled Residue Count: 821
Deposited Residue Count: 856
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	A [auth H]	266	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for Q3J170 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J170 Go to UniProtKB: Q3J170
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J170
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	282	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for Q3J1A5 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A5 Go to UniProtKB: Q3J1A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J1A5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	308	Cereibacter sphaeroides	Mutation(s): 1 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A6 Go to UniProtKB: Q3J1A6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J1A6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download:Ideal Coordinates CCD File SDF format, chain Q [auth M] MOL2 format, chain Q [auth M] mmCIF format, chain Q [auth M]	Q [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain Q [auth M] Interactions & Density Focus chain Q [auth M]
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain K [auth M] SDF format, chain J [auth M] SDF format, chain G [auth L] SDF format, chain D [auth L] MOL2 format, chain K [auth M] MOL2 format, chain J [auth M] MOL2 format, chain G [auth L] MOL2 format, chain D [auth L] mmCIF format, chain K [auth M] mmCIF format, chain J [auth M] mmCIF format, chain G [auth L] mmCIF format, chain D [auth L]	D [auth L], G [auth L], J [auth M], K [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain D [auth L] Focus chain G [auth L] Focus chain J [auth M] Focus chain K [auth M] Interactions & Density Focus chain D [auth L] Focus chain G [auth L] Focus chain J [auth M] Focus chain K [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download:Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain E [auth L] MOL2 format, chain H [auth L] MOL2 format, chain E [auth L] mmCIF format, chain H [auth L] mmCIF format, chain E [auth L]	E [auth L], H [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain E [auth L] Focus chain H [auth L] Interactions & Density Focus chain E [auth L] Focus chain H [auth L]
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain F [auth L] MOL2 format, chain F [auth L] mmCIF format, chain F [auth L]	F [auth L]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain F [auth L] Interactions & Density Focus chain F [auth L]
SPO Query on SPO 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]	SPHEROIDENE C₄₁ H₆₀ O FJOCMTHZSURUFA-KXCOHNEYSA-N		Interactions Focus chain P [auth M] Interactions & Density Focus chain P [auth M]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain N [auth M] SDF format, chain M SDF format, chain L [auth M] MOL2 format, chain N [auth M] MOL2 format, chain M MOL2 format, chain L [auth M] mmCIF format, chain N [auth M] mmCIF format, chain M mmCIF format, chain L [auth M]	L [auth M], M, N [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain L [auth M] Focus chain M Focus chain N [auth M] Interactions & Density Focus chain L [auth M] Focus chain M Focus chain N [auth M]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain O [auth M] MOL2 format, chain O [auth M] mmCIF format, chain O [auth M]	O [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain O [auth M] Interactions & Density Focus chain O [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L] mmCIF format, chain I [auth L]	I [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.178 (Depositor), 0.185 (DCC)
R-Value Work: 0.156 (Depositor), 0.164 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.193	α = 90
b = 142.193	β = 90
c = 187.673	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-27

Deposition Author(s):

Boxer, S.G.

Mathews, I.I.

Weaver, J.B.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133894