1ZVF | pdb_00001zvf

The crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb1ZVF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-06-02 Released: 2006-06-02 
• Deposition Author(s): Li, X., Guo, M., Teng, M., Niu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.268 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

The crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from Saccharomyces cerevisiae

Li, X., Guo, M., Teng, M., Niu, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.61 kDa 
• Atom Count: 2,874 
• Modeled Residue Count: 348 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyanthranilate 3,4-dioxygenase	A, B	176	Saccharomyces cerevisiae	Mutation(s): 0  EC: 1.13.11.6
UniProt
Find proteins for P47096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47096  Go to UniProtKB:  P47096

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth A], E [auth B], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.268 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.104	α = 90
b = 66.195	β = 90
c = 130.188	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-02 
Deposition Author(s): Li, X., Guo, M., Teng, M., Niu, L.

Revision History  

• Version 1.0: 2006-06-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations