2YQB

Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 A resolution

Structural Biology Knowledgebase: 2YQB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.147
  • R-Value Work: 0.112

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YQB

Classification: OXIDOREDUCTASE

Total Structure Weight: 50666.63

Macromolecule Entities
Molecule Chains Length Organism Details
COPPER-CONTAINING NITRITE REDUCTASE A 468 Ralstonia pickettii EC#: 1.7.2.1 IUBMB
Mutation: P93A
Gene Name(s): Rpic_4015
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

A COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.147
  • R-Value Work: 0.112
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.85 α = 90.00
b = 127.85 β = 90.00
c = 86.63 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-07
  • Released Date: 2013-04-03
  • Deposition author(s): Antonyuk, S.V., Han, C., Eady, R.R., Hasnain, S.S.

Revision History

  • 2013-04-17
    Type: Citation | Details: JRNL