1VF5

Crystal Structure of Cytochrome b6f Complex from M.laminosus

Structural Biology Knowledgebase: 1VF5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.346
  • R-Value Work: 0.258

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1VF5

Classification: PHOTOSYNTHESIS

Total Structure Weight: 228943.22

Macromolecule Entities
Molecule Chains Length Organism Details
CYTOCHROME B6 A, N 215 Mastigocladus laminosus Gene Name(s): petB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUBUNIT IV B, O 160 Mastigocladus laminosus Gene Name(s): petD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME F C, P 289 Mastigocladus laminosus Gene Name(s): petA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RIESKE IRON-SULFUR PROTEIN D, Q 179 Mastigocladus laminosus EC#: 1.10.9.1 IUBMB
Gene Name(s): petC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN PET L E, R 32 Mastigocladus laminosus Gene Name(s): petL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN PET M F, S 35 Mastigocladus laminosus Gene Name(s): petM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN PET G G, T 37 Mastigocladus laminosus Gene Name(s): petG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN PET N H, U 29 Mastigocladus laminosus Gene Name(s): petN
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis

Protein Name: Cytochrome b6f complex


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

B, O CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OPC
Query on OPC

B, D, N, Q (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7- [(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA- 4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
DIOLEOYL-PHOSPHATIDYLCHOLINE (Synonym)
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PL9
Query on PL9

A, Q 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35- NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL- 2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL- 5-SOLANESYL-1,4-BENZOQUINONE
PLASTOQUINONE 9 (Synonym)
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

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

E, R BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TDS
Query on TDS

A, N 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL- 4H-CHROMEN-4-ONE
TRIDECYL-STIGMATELLIN (Synonym)
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

D, Q FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.346
  • R-Value Work: 0.258
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 157.54 α = 90.00
b = 157.54 β = 90.00
c = 360.35 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-08
  • Released Date: 2004-04-20
  • Deposition author(s): Kurisu, G., Zhang, H., Smith, J.L., Cramer, W.A.
  • Previous versions: 1UM3

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4