4LWY

L(M196)H,H(M202)L Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV

PDB DOI: https://doi.org/10.2210/pdb4LWY/pdb

Classification: electron transport, membrane protein
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2013-07-29 Released: 2014-07-16
Deposition Author(s): Gabdulkhakov, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.216

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular Dynamic Studies of Reaction Centers Mutants from Rhodobacter sphaeroides and his mutant form L(M196)H+H(M202)L

Kljashtorny, V.G., Fufina, T.Y., Vasilieva, L.G., Gabdulkhakov, A.G.

(2014) Crystallogr Rep 59: 536-541

Macromolecule Content

Total Structure Weight: 105.55 kDa
Atom Count: 7,434
Modelled Residue Count: 823
Deposited Residue Count: 845
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	A [auth H]	260	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

Find similar proteins by:

(by identity cutoff) | 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 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]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain CA [auth M] MOL2 format, chain CA [auth M] mmCIF format, chain CA [auth M]	CA [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain CA [auth M] Interactions & Density Focus chain CA [auth M]
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain EA [auth M] SDF format, chain Q [auth L] SDF format, chain R [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] mmCIF format, chain EA [auth M] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L]	EA [auth M], Q [auth L], R [auth L]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain EA [auth M] Focus chain Q [auth L] Focus chain R [auth L] Interactions & Density Focus chain EA [auth M] Focus chain Q [auth L] Focus chain R [auth L]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain DA [auth M] SDF format, chain FA [auth M] SDF format, chain S [auth L] MOL2 format, chain DA [auth M] MOL2 format, chain FA [auth M] MOL2 format, chain S [auth L] mmCIF format, chain DA [auth M] mmCIF format, chain FA [auth M] mmCIF format, chain S [auth L]	DA [auth M], FA [auth M], S [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain DA [auth M] Focus chain FA [auth M] Focus chain S [auth L] Interactions & Density Focus chain DA [auth M] Focus chain FA [auth M] Focus chain S [auth L]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain HA [auth M] SDF format, chain T [auth L] MOL2 format, chain HA [auth M] MOL2 format, chain T [auth L] mmCIF format, chain HA [auth M] mmCIF format, chain T [auth L]	HA [auth M], T [auth L]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain HA [auth M] Focus chain T [auth L] Interactions & Density Focus chain HA [auth M] Focus chain T [auth L]
SPN Query on SPN Download Ideal Coordinates CCD File SDF format, chain IA [auth M] MOL2 format, chain IA [auth M] mmCIF format, chain IA [auth M]	IA [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain IA [auth M] Interactions & Density Focus chain IA [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain JA [auth M] SDF format, chain LA [auth M] SDF format, chain NA [auth M] SDF format, chain KA [auth M] SDF format, chain MA [auth M] MOL2 format, chain D [auth H] MOL2 format, chain JA [auth M] MOL2 format, chain LA [auth M] MOL2 format, chain NA [auth M] MOL2 format, chain KA [auth M] MOL2 format, chain MA [auth M] mmCIF format, chain D [auth H] mmCIF format, chain JA [auth M] mmCIF format, chain LA [auth M] mmCIF format, chain NA [auth M] mmCIF format, chain KA [auth M] mmCIF format, chain MA [auth M]	D [auth H] JA [auth M] KA [auth M] LA [auth M] MA [auth M] D [auth H], JA [auth M], KA [auth M], LA [auth M], MA [auth M], NA [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain JA [auth M] Focus chain KA [auth M] Focus chain LA [auth M] Focus chain MA [auth M] Focus chain NA [auth M] Interactions & Density Focus chain D [auth H] Focus chain JA [auth M] Focus chain KA [auth M] Focus chain LA [auth M] Focus chain MA [auth M] Focus chain NA [auth M]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth L] SDF format, chain O [auth H] MOL2 format, chain BA [auth L] MOL2 format, chain O [auth H] mmCIF format, chain BA [auth L] mmCIF format, chain O [auth H]	BA [auth L], O [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth L] Focus chain O [auth H] Interactions & Density Focus chain BA [auth L] Focus chain O [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain RA [auth M] SDF format, chain SA [auth M] MOL2 format, chain I [auth H] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth M] mmCIF format, chain I [auth H] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth M]	I [auth H], RA [auth M], SA [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth H] Focus chain RA [auth M] Focus chain SA [auth M] Interactions & Density Focus chain I [auth H] Focus chain RA [auth M] Focus chain SA [auth M]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain TA [auth M] SDF format, chain Y [auth L] SDF format, chain Z [auth L] MOL2 format, chain J [auth H] MOL2 format, chain TA [auth M] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth L] mmCIF format, chain J [auth H] mmCIF format, chain TA [auth M] mmCIF format, chain Y [auth L] mmCIF format, chain Z [auth L]	J [auth H], TA [auth M], Y [auth L], Z [auth L]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain TA [auth M] Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain J [auth H] Focus chain TA [auth M] Focus chain Y [auth L] Focus chain Z [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain UA [auth M] SDF format, chain VA [auth M] MOL2 format, chain AA [auth L] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain UA [auth M] MOL2 format, chain VA [auth M] mmCIF format, chain AA [auth L] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain UA [auth M] mmCIF format, chain VA [auth M]	AA [auth L] K [auth H] L [auth H] M [auth H] N [auth H] AA [auth L], K [auth H], L [auth H], M [auth H], N [auth H], UA [auth M], VA [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain UA [auth M] Focus chain VA [auth M] Interactions & Density Focus chain AA [auth L] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain UA [auth M] Focus chain VA [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain GA [auth M] MOL2 format, chain GA [auth M] mmCIF format, chain GA [auth M]	GA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain GA [auth M] Interactions & Density Focus chain GA [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H] mmCIF format, chain P [auth H]	P [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Interactions & Density Focus chain P [auth H]
UNL Query on UNL Download Ideal Coordinates CCD File	E [auth H] F [auth H] G [auth H] H OA [auth M] E [auth H], F [auth H], G [auth H], H, OA [auth M], PA [auth M], QA [auth M], U [auth L], V [auth L], W [auth L], X [auth L]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain OA [auth M] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain OA [auth M] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.04	α = 90
b = 140.04	β = 90
c = 184.62	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Gabdulkhakov, A.G.

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description