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


Ligand Structure Quality Assessment 


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 
UniProt
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
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G43875TD
GlyCosmos:  G43875TD
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
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

View Full Validation Report



Ligand Structure Quality Assessment  



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