5V26 | pdb_00005v26

1.78 angstrom crystal structure of P97H 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans

• PDB DOI: https://doi.org/10.2210/pdb5V26/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cupriavidus metallidurans CH34
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-02 Released: 2018-03-07 
• Deposition Author(s): Dornevil, K., Liu, F., Liu, A.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

1.78 angstrom crystal structure of P97H 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans

Dornevil, K., Liu, F., Liu, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.47 kDa 
• Atom Count: 3,067 
• Modeled Residue Count: 343 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyanthranilate 3,4-dioxygenase	A, B	201	Cupriavidus metallidurans CH34	Mutation(s): 1  Gene Names: nbaC, Rmet_5193 EC: 1.13.11.6
UniProt
Find proteins for Q1LCS4 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)) Explore Q1LCS4  Go to UniProtKB:  Q1LCS4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	C [auth A], D [auth A], E [auth B], F [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.229	α = 90
b = 57.692	β = 103.82
c = 79.501	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Dornevil, K., Liu, F., Liu, A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1623856
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R21MH107985

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description