7Z8D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainA [auth H]242Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]281Cereibacter sphaeroides 2.4.1Mutation(s): 1 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]302Cereibacter sphaeroides 2.4.1Mutation(s): 1 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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E [auth L],
F [auth L],
O [auth M],
P [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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G [auth L],
Q [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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N [auth M]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPN (Subject of Investigation/LOI)
Query on SPN

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S [auth M]SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
NKP
Query on NKP

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K [auth M],
L [auth M]
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
C21 H41 O7 P
WRGQSWVCFNIUNZ-SQUSKLHYSA-N
OLC
Query on OLC

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J [auth L](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
LDA
Query on LDA

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D [auth H],
M,
T [auth M],
U [auth M],
V [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
MYS
Query on MYS

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I [auth L]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
D12
Query on D12

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H [auth L],
W [auth M]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
PO4
Query on PO4

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Y [auth M]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

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X [auth M]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

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R [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.5α = 90
b = 102.5β = 90
c = 237.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation18-02-40008_mega

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description