5OBO

Crystal structure of nitrite bound D97N mutant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases

Dong, J.Sasaki, D.Eady, R.Antonyuk, S.V.Hasnain, S.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrite reductase, copper-containing468Ralstonia sp. 5_2_56FAAMutation(s): 1 
Gene Names: HMPREF0989_00586
UniProt
Find proteins for U3G913 (Ralstonia sp. 5_2_56FAA)
Explore U3G913 
Go to UniProtKB:  U3G913
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU3G913
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
GOL
Query on GOL

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E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

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B [auth A],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2
Query on NO2

Download Ideal Coordinates CCD File 
G [auth A]NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.69α = 90
b = 180.69β = 90
c = 180.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L006960/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description