5OBO | pdb_00005obo

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

• PDB DOI: https://doi.org/10.2210/pdb5OBO/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Ralstonia sp. 5_2_56FAA
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-06-28 Released: 2018-08-01 
• Deposition Author(s): Dong, J., Sasaki, D., Eady, R., Antonyuk, S.V., Hasnain, S.S.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.92 kDa 
• Atom Count: 4,506 
• Modeled Residue Count: 456 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite reductase, copper-containing	A	468	Ralstonia sp. 5_2_56FAA	Mutation(s): 1  Gene Names: HMPREF0989_00586

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	D [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2	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 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.69	α = 90
b = 180.69	β = 90
c = 180.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Dong, J., Sasaki, D., Eady, R., Antonyuk, S.V., Hasnain, S.S.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/L006960/1

Revision History  

• 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