4WZC | pdb_00004wzc

Understanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Catalytic Intermediates - 2,3-cis-4,5-trans ACMS bound to I142A mutant HAO

• PDB DOI: https://doi.org/10.2210/pdb4WZC/pdb

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


• Deposited: 2014-11-19 Released: 2016-02-10 
• Deposition Author(s): Liu, F., Liu, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Probing Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Reaction Cycle Intermediates

Liu, F., Liu, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.73 kDa 
• Atom Count: 1,516 
• Modeled Residue Count: 174 
• Deposited Residue Count: 177 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyanthranilate 3,4-dioxygenase	A	177	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1UC	D [auth A]	(2E)-2-amino-3-[(1E)-3-oxoprop-1-en-1-yl]but-2-enedioic acid C7 H7 N O5 KACPVQQHDVBVFC-PMRVSPHWSA-N
FE2	B [auth A], C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.282	α = 90
b = 58.282	β = 90
c = 230.605	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Liu, F., Liu, A.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Non-polymer description
• Version 1.2: 2017-08-09
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description