4YSU

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 25.0 MGy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 4YSU

Classification: OXIDOREDUCTASE

Total Structure Weight: 36055.03

Macromolecule Entities
Molecule Chains Length Organism Details
Nitrite reductase A 323 Geobacillus thermodenitrificans Fragment: UNP residues 31-352
Gene Name(s): nirK GTNG_0650
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.163
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 115.21 α = 90.00
b = 115.21 β = 90.00
c = 84.39 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-03-17
  • Released Date: 2016-02-24
  • Deposition author(s): Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

Revision History

  • 2016-05-25
    Type: Database references