4R52 | pdb_00004r52

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

• PDB DOI: https://doi.org/10.2210/pdb4R52/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cupriavidus metallidurans CH34
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-20 Released: 2016-03-02 
• Deposition Author(s): Geng, J., Gumpper, R.H., Huo, L., Liu, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.214 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

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

Geng, J., Gumpper, R.H., Huo, L., Liu, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.29 kDa 
• Atom Count: 1,605 
• Modeled Residue Count: 174 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyanthranilate 3,4-dioxygenase	A	174	Cupriavidus metallidurans CH34	Mutation(s): 0  Gene Names: nbaC, nbaC Rmet_5193, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
FE2	B [auth A], C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.214 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.32	α = 90
b = 58.32	β = 90
c = 231.849	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Geng, J., Gumpper, R.H., Huo, L., Liu, A.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description