1Z1N

Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas

Santos-Silva, T.Dias, J.M.Romao, M.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
sixteen heme cytochromeA [auth X]560Desulfovibrio gigasMutation(s): 0 
Find proteins for T2G9Q2 (Desulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759))
Explore T2G9Q2 
Go to UniProtKB:  T2G9Q2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
F [auth X] , G [auth X] , H [auth X] , I [auth X] , J [auth X] , K [auth X] , L [auth X] , M [auth X] , 
F [auth X],  G [auth X],  H [auth X],  I [auth X],  J [auth X],  K [auth X],  L [auth X],  M [auth X],  N [auth X],  O [auth X],  P [auth X],  Q [auth X],  R [auth X],  S [auth X],  T [auth X],  U [auth X]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
V [auth X], W [auth X], X, Y [auth X], Z [auth X]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth X], D [auth X], E [auth X]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.889α = 90
b = 90.799β = 90
c = 83.934γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary