1Q0D

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state

Structural Biology Knowledgebase: 1Q0D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Q0D

Classification: OXIDOREDUCTASE

Total Structure Weight: 160738.52

Macromolecule Entities
Molecule Chains Length Organism Details
Superoxide dismutase [Ni] A, B, C..., D, E, F, G, H, I, J, K, LA, B, C, D, E, F, G, H, I, J, K, L 117 Streptomyces seoulensis EC#: 1.15.1.1 IUBMB
Details: THE ASYMMETRIC UNIT CONTAINS TWO HEXAMERS
Gene Name(s): sodN

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B, C, D, E, F, G, H, I, J, K, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3NI
Query on 3NI

A, B, C, D, E, F, G, H, I, J, K, L NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.172
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 112.26 α = 90.00
b = 113.75 β = 90.00
c = 128.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-16
  • Released Date: 2004-05-18
  • Deposition author(s): Wuerges, J., Lee, J.-W., Yim, Y.-I., Yim, H.-S., Kang, S.-O., Djinovic Carugo, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4