1YW0 | pdb_00001yw0

Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.

• PDB DOI: https://doi.org/10.2210/pdb1YW0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-16 Released: 2005-03-15 
• Deposition Author(s): Vorobiev, S.M., Abashidze, M., Forouhar, F., Kuzin, A., Xiao, R., Ciano, M., Aton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.294 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Literature

Crystal structure of the tryptophan 2,3-dioxygenase from Xanthomonas campestris. Northeast Structural Genomics Target XcR13.

Vorobiev, S.M., Abashidze, M., Forouhar, F., Kuzin, A., Xiao, R., Ciano, M., Aton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 129.75 kDa 
• Atom Count: 8,274 
• Modeled Residue Count: 971 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tryptophan 2,3-dioxygenase	A, B, C, D	276	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 5  EC: 1.13.11.11
UniProt
Find proteins for Q8PDA8 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PDA8  Go to UniProtKB:  Q8PDA8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.294 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.701	α = 90
b = 110.223	β = 90
c = 149.398	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Vorobiev, S.M., Abashidze, M., Forouhar, F., Kuzin, A., Xiao, R., Ciano, M., Aton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-03-15
  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: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary