2ZT9

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120

Structural Biology Knowledgebase: 2ZT9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZT9

Classification: PHOTOSYNTHESIS

Total Structure Weight: 114202.13

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome b6 A 215 Nostoc sp. pcc 7120 Gene Name(s): petB alr3421
Cytochrome b6-f complex subunit 4 B 160 Nostoc sp. pcc 7120 Gene Name(s): petD alr3422
Apocytochrome f C 289 Nostoc sp. pcc 7120 Gene Name(s): petA all2452
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
Cytochrome b6-f complex subunit 6 E 31 Nostoc sp. pcc 7120 Gene Name(s): petL asl1922
Cytochrome b6-f complex subunit 7 F 34 Nostoc sp. pcc 7120 Gene Name(s): petM asl4754
Cytochrome b6-f complex subunit 5 G 37 Nostoc sp. pcc 7120 Gene Name(s): petG asr1366
Cytochrome b6-f complex subunit 8 H 29 Nostoc sp. pcc 7120 Gene Name(s): petN asl4263

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

B, H (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

B 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)
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 UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE (Synonym)
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.230
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 159.23 α = 90.00
b = 159.23 β = 90.00
c = 365.89 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-27
  • Released Date: 2009-02-10
  • Deposition author(s): Craner, W.A., Baniulis D., Yamashita E.

Revision History

  • 2013-12-11
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4