7Z8D

Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV)

PDB DOI: https://doi.org/10.2210/pdb7Z8D/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Cereibacter sphaeroides 2.4.1
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2022-03-17 Released: 2023-03-29
Deposition Author(s): Gabdulkhakov, A.G., Selikhanov, G.K., Guenther, S., Petrova, T., Meents, A., Fufina, T.Y., Vasilieva, L.G.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

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

Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 26keV)

Gabdulkhakov, A.G., Selikhanov, G.K., Guenther, S., Meents, A., Fufina, T.Y., Vasilieva, L.G.

To be published.

Macromolecule Content

Total Structure Weight: 101.56 kDa
Atom Count: 7,660
Modelled Residue Count: 825
Deposited Residue Count: 825
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]	242	Cereibacter sphaeroides 2.4.1	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 LOADING

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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 2.4.1	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 LOADING

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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]	302	Cereibacter sphaeroides 2.4.1	Mutation(s): 1 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 LOADING

Small Molecules

Ligands 12 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 E [auth L] SDF format, chain F [auth L] SDF format, chain O [auth M] SDF format, chain P [auth M] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain O [auth M] MOL2 format, chain P [auth M] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain O [auth M] mmCIF format, chain P [auth M]	E [auth L], F [auth L], O [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 O [auth M] Focus chain P [auth M] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain O [auth M] Focus chain P [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain Q [auth M] MOL2 format, chain G [auth L] MOL2 format, chain Q [auth M] mmCIF format, chain G [auth L] mmCIF format, chain Q [auth M]	G [auth L], Q [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain G [auth L] Focus chain Q [auth M] Interactions & Density Focus chain G [auth L] Focus chain Q [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain N [auth M] MOL2 format, chain N [auth M] mmCIF format, chain N [auth M]	N [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]
SPN (Subject of Investigation/LOI) Query on SPN Download Ideal Coordinates CCD File SDF format, chain S [auth M] MOL2 format, chain S [auth M] mmCIF format, chain S [auth M]	S [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain S [auth M] Interactions & Density Focus chain S [auth M]
NKP Query on NKP Download Ideal Coordinates CCD File SDF format, chain K [auth M] SDF format, chain L [auth M] MOL2 format, chain K [auth M] MOL2 format, chain L [auth M] mmCIF format, chain K [auth M] mmCIF format, chain L [auth M]	K [auth M], L [auth M]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C₂₁ H₄₁ O₇ P WRGQSWVCFNIUNZ-SQUSKLHYSA-N		Interactions Focus chain K [auth M] Focus chain L [auth M] Interactions & Density Focus chain K [auth M] Focus chain L [auth M]
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain J [auth L] MOL2 format, chain J [auth L] mmCIF format, chain J [auth L]	J [auth L]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain J [auth L] Interactions & Density Focus chain J [auth L]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain M SDF format, chain T [auth M] SDF format, chain U [auth M] SDF format, chain V [auth M] MOL2 format, chain D [auth H] MOL2 format, chain M MOL2 format, chain T [auth M] MOL2 format, chain U [auth M] MOL2 format, chain V [auth M] mmCIF format, chain D [auth H] mmCIF format, chain M mmCIF format, chain T [auth M] mmCIF format, chain U [auth M] mmCIF format, chain V [auth M]	D [auth H], M, T [auth M], U [auth M], V [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain M Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M] Interactions & Density Focus chain D [auth H] Focus chain M Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M]
MYS Query on MYS 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]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain W [auth M] MOL2 format, chain H [auth L] MOL2 format, chain W [auth M] mmCIF format, chain H [auth L] mmCIF format, chain W [auth M]	H [auth L], W [auth M]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain W [auth M] Interactions & Density Focus chain H [auth L] Focus chain W [auth M]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth M] MOL2 format, chain Y [auth M] mmCIF format, chain Y [auth M]	Y [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain Y [auth M] Interactions & Density Focus chain Y [auth M]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain X [auth M] MOL2 format, chain X [auth M] mmCIF format, chain X [auth M]	X [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain X [auth M] Interactions & Density Focus chain X [auth M]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain R [auth M] MOL2 format, chain R [auth M] mmCIF format, chain R [auth M]	R [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain R [auth M] Interactions & Density Focus chain R [auth M]