7P17 | pdb_00007p17

F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (room temperature, 12keV)

PDB DOI: https://doi.org/10.2210/pdb7P17/pdb

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

Deposited: 2021-07-01 Released: 2022-07-13
Deposition Author(s): Gabdulkhakov, A.G., Selikhanov, G.K., Guenther, S., Meents, A., Fufina, T.Y., Vasilieva, L.G.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.215 (Depositor), 0.221 (DCC)
R-Value Work:
0.177 (Depositor), 0.181 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-Ray structure of Rhodobacter sphaeroides reaction center with M197 Phe-His substitution clarifies properties of the mutant complex

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

To be published.

Macromolecule Content

Total Structure Weight: 101.19 kDa
Atom Count: 7,589
Modeled Residue Count: 824
Deposited Residue Count: 826
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]	242	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0Y7
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]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0Y8
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]	303	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 S [auth M] SDF format, chain R [auth M] SDF format, chain K [auth L] SDF format, chain J [auth L] MOL2 format, chain S [auth M] MOL2 format, chain R [auth M] MOL2 format, chain K [auth L] MOL2 format, chain J [auth L] mmCIF format, chain S [auth M] mmCIF format, chain R [auth M] mmCIF format, chain K [auth L] mmCIF format, chain J [auth L]	J [auth L], K [auth L], R [auth M], S [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain J [auth L] Focus chain K [auth L] Focus chain R [auth M] Focus chain S [auth M] Interactions & Density Focus chain J [auth L] Focus chain K [auth L] Focus chain R [auth M] Focus chain S [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download:Ideal Coordinates CCD File SDF format, chain M [auth L] SDF format, chain L MOL2 format, chain M [auth L] MOL2 format, chain L mmCIF format, chain M [auth L] mmCIF format, chain L	L, M [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain L Focus chain M [auth L] Interactions & Density Focus chain L Focus chain M [auth L]
U10 Query on U10 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]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain O [auth M] Interactions & Density Focus chain O [auth M]
SPN Query on SPN 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]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain Q [auth M] Interactions & Density Focus chain Q [auth M]
NKP Query on NKP Download:Ideal Coordinates CCD File SDF format, chain N [auth M] SDF format, chain P [auth M] MOL2 format, chain N [auth M] MOL2 format, chain P [auth M] mmCIF format, chain N [auth M] mmCIF format, chain P [auth M]	N [auth M], P [auth M]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C₂₁ H₄₁ O₇ P WRGQSWVCFNIUNZ-SQUSKLHYSA-N		Interactions Focus chain N [auth M] Focus chain P [auth M] Interactions & Density Focus chain N [auth M] Focus chain P [auth M]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L] mmCIF format, chain G [auth L]	G [auth L]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain U [auth M] SDF format, chain E [auth H] MOL2 format, chain U [auth M] MOL2 format, chain E [auth H] mmCIF format, chain U [auth M] mmCIF format, chain E [auth H]	E [auth H], U [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain U [auth M] Interactions & Density Focus chain E [auth H] Focus chain U [auth M]
MYS Query on MYS Download:Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain H [auth L] SDF format, chain F [auth H] SDF format, chain D [auth H] MOL2 format, chain I [auth L] MOL2 format, chain H [auth L] MOL2 format, chain F [auth H] MOL2 format, chain D [auth H] mmCIF format, chain I [auth L] mmCIF format, chain H [auth L] mmCIF format, chain F [auth H] mmCIF format, chain D [auth H]	D [auth H], F [auth H], H [auth L], I [auth L]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain F [auth H] Focus chain H [auth L] Focus chain I [auth L] Interactions & Density Focus chain D [auth H] Focus chain F [auth H] Focus chain H [auth L] Focus chain I [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth M] MOL2 format, chain V [auth M] mmCIF format, chain V [auth M]	V [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain V [auth M] Interactions & Density Focus chain V [auth M]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain T [auth M] MOL2 format, chain T [auth M] mmCIF format, chain T [auth M]	T [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain T [auth M] Interactions & Density Focus chain T [auth M]