1L9J

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

Structural Biology Knowledgebase: 1L9J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.248

Literature

Macromolecules
Sequence Display for 1L9J

Classification: PHOTOSYNTHESIS

Total Structure Weight: 229509.34

Macromolecule Entities
Molecule Chains Length Organism Details
REACTION CENTER PROTEIN L CHAIN L, R 281 Rhodobacter sphaeroides Gene Name(s): pufL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
REACTION CENTER PROTEIN M CHAIN M, S 307 Rhodobacter sphaeroides Gene Name(s): pufM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
REACTION CENTER PROTEIN H CHAIN H, T 260 Rhodobacter sphaeroides Gene Name(s): puhA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
cytochrome c-2 C, D 124 Rhodobacter sphaeroides Gene Name(s): cycA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Photosynthetic Reaction Centers

Protein Name: Photosynthetic Reaction Center


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BCL
Query on BCL

L, M, R, S BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BPH
Query on BPH

L, M, R, S BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
U10
Query on U10

M, S UBIQUINONE-10
Coenzyme Q10 (Synonym)
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LDA
Query on LDA

M, S LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

M, S FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

M, S CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.248
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 77.93 α = 90.00
b = 80.31 β = 92.41
c = 246.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-03-24
  • Released Date: 2002-06-12
  • Deposition author(s): Axelrod, H.L., Abresch, E.C., Okamura, M.Y., Yeh, A.P., Rees, D.C., Feher, G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update