3ML1

Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.157

Literature

Macromolecules
Sequence Display for 3ML1

Classification: OXIDOREDUCTASE

Total Structure Weight: 109135.66

Macromolecule Entities
Molecule Chains Length Organism Details
Periplasmic nitrate reductase A 802 Cupriavidus necator EC#: 1.7.99.4 IUBMB
Details: Catalytic subunit
Gene Name(s): napA PHG211
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Diheme cytochrome c napB B 135 Cupriavidus necator EC#: 1.9.6.1 IUBMB
Gene Name(s): napB PHG212
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MGD
Query on MGD

A 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym)
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEC
Query on HEC

B HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MOS
Query on MOS

A DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.157
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 142.20 α = 90.00
b = 82.38 β = 100.72
c = 96.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-04-16
  • Released Date: 2011-04-06
  • Deposition author(s): Coelho, C., Trincao, J., Romao, M.J.

Revision History

  • Version 1_0: 2011-04-06

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2011-12-07

    Type: Database references