4H13

Crystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS

Structural Biology Knowledgebase: 4H13 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 4H13

Classification: PHOTOSYNTHESIS

Total Structure Weight: 117210.55

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome b6 A 215 Mastigocladus laminosus Gene Name(s): petB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 4 B 160 Mastigocladus laminosus Gene Name(s): petD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Apocytochrome f C 289 Mastigocladus laminosus Mutation: E11P
Gene Name(s): petA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex iron-sulfur subunit D 179 Mastigocladus laminosus EC#: 1.10.9.1 IUBMB
Gene Name(s): petC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 6 E 32 Mastigocladus laminosus Gene Name(s): petL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 7 F 35 Mastigocladus laminosus Gene Name(s): petM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 5 G 37 Mastigocladus laminosus Gene Name(s): petG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b6-f complex subunit 8 H 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 13 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OPC
Query on OPC

A, B (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 NGL
 
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 NGL
 
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 NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

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

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

A, B 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL- 4H-CHROMEN-4-ONE
TRIDECYL-STIGMATELLIN (Synonym)
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
8K6
Query on 8K6

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

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

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.214
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 157.20 α = 90.00
b = 157.20 β = 90.00
c = 363.28 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-10
  • Released Date: 2013-02-13
  • Deposition author(s): Hasan, S.S., Yamashita, E., Baniulis, D., Cramer, W.A.

Revision History

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