2ZOO | pdb_00002zoo

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

• PDB DOI: https://doi.org/10.2210/pdb2ZOO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudoalteromonas translucida TAC125
• Mutation(s): No 


• Deposited: 2008-05-27 Released: 2009-06-09 
• Deposition Author(s): Nojiri, M., Tsuda, A., Yamaguchi, K., Suzuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Models: experimental

Literature

Electron transfer processes within and between proteins containing the HEME C and blue Cu

Nojiri, M., Koteishi, H., Tsuda, A., Nakagami, T., Kobayashi, K., Inoue, T., Yamaguchi, K., Suzuki, 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)

Macromolecule Content 

• Total Structure Weight: 48.99 kDa 
• Atom Count: 3,811 
• Modeled Residue Count: 438 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nitrite reductase	A	442	Pseudoalteromonas translucida TAC125	Mutation(s): 0  EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (PDB Primary Data)
UniProt
Find proteins for Q3IGF7 (Pseudoalteromonas translucida (strain TAC 125)) Explore Q3IGF7  Go to UniProtKB:  Q3IGF7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU	C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.338	α = 90
b = 180.338	β = 90
c = 180.338	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Nojiri, M., Tsuda, A., Yamaguchi, K., Suzuki, S.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary