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
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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

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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]	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

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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]	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

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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]	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 R [auth L] SDF format, chain Q [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain R [auth L] MOL2 format, chain Q [auth L] mmCIF format, chain EA [auth M] mmCIF format, chain R [auth L] mmCIF format, chain Q [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 KA [auth M] SDF format, chain LA [auth M] SDF format, chain MA [auth M] SDF format, chain NA [auth M] SDF format, chain JA [auth M] MOL2 format, chain D [auth H] MOL2 format, chain KA [auth M] MOL2 format, chain LA [auth M] MOL2 format, chain MA [auth M] MOL2 format, chain NA [auth M] MOL2 format, chain JA [auth M] mmCIF format, chain D [auth H] mmCIF format, chain KA [auth M] mmCIF format, chain LA [auth M] mmCIF format, chain MA [auth M] mmCIF format, chain NA [auth M] mmCIF format, chain JA [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 RA [auth M] SDF format, chain SA [auth M] SDF format, chain I [auth H] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth M] MOL2 format, chain I [auth H] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth M] mmCIF format, chain I [auth H]	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 Z [auth L] SDF format, chain Y [auth L] MOL2 format, chain J [auth H] MOL2 format, chain TA [auth M] MOL2 format, chain Z [auth L] MOL2 format, chain Y [auth L] mmCIF format, chain J [auth H] mmCIF format, chain TA [auth M] mmCIF format, chain Z [auth L] mmCIF format, chain Y [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 K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain VA [auth M] SDF format, chain AA [auth L] SDF format, chain UA [auth M] 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 VA [auth M] MOL2 format, chain AA [auth L] MOL2 format, chain UA [auth M] 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 VA [auth M] mmCIF format, chain AA [auth L] mmCIF format, chain UA [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

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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