4H44

2.70 A Cytochrome b6f Complex Structure From Nostoc PCC 7120

Structural Biology Knowledgebase: 4H44 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H44

Classification: PHOTOSYNTHESIS

Total Structure Weight: 116453.72

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome b6 A 215 Nostoc sp. pcc 7120 Gene Name(s): petB alr3421
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 4 B 160 Nostoc sp. pcc 7120 Gene Name(s): petD alr3422
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Apocytochrome f C 289 Nostoc sp. pcc 7120 Gene Name(s): petA all2452
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex iron-sulfur subunit 1 D 179 Nostoc sp. pcc 7120 EC#: 1.10.9.1 IUBMB
Gene Name(s): petC1 all2453
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 6 E 31 Nostoc sp. pcc 7120 Gene Name(s): petL asl1922
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 7 F 34 Nostoc sp. pcc 7120 Gene Name(s): petM asl4754
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 5 G 37 Nostoc sp. pcc 7120 Gene Name(s): petG asr1366
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 8 H 29 Nostoc sp. pcc 7120 Gene Name(s): petN asl4263
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 12 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLA
Query on CLA

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

B, C (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)
SQD
Query on SQD

D 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA- D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL (Synonym)
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

A, C PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
7PH
Query on 7PH

C (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
PHOSPHATIDIC ACID (Synonym)
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

G BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMQ
Query on UMQ

A, F UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE (Synonym)
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
8K6
Query on 8K6

A Octadecane
N-Octadecane (Synonym)
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MYS
Query on MYS

A PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

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

F N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

C CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.220
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 159.13 α = 90.00
b = 159.13 β = 90.00
c = 364.37 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-16
  • Released Date: 2013-02-20
  • Deposition author(s): Hasan, S.S., Yamashita, E., Baniulis, D., Cramer, W.A.

Revision History

  • 2013-04-03
    Type: Citation | Details: Citation update