3DTY | pdb_00003dty

Crystal structure of an Oxidoreductase from Pseudomonas syringae

• PDB DOI: https://doi.org/10.2210/pdb3DTY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas syringae pv. tomato
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-16 Released: 2008-08-05 
• Deposition Author(s): Eswaramoorthy, S., Mahmood, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of an Oxidoreductase from Pseudomonas syringae

Eswaramoorthy, S., Mahmood, A., Burley, S.K., Swaminathan, S.

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: 179.17 kDa 
• Atom Count: 12,349 
• Modeled Residue Count: 1,474 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B, C [auth D], D [auth E]	398	Pseudomonas syringae pv. tomato	Mutation(s): 0  Gene Names: PSPTO3019, PSPTO_3019
UniProt
Find proteins for Q880Y1 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q880Y1  Go to UniProtKB:  Q880Y1

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.281	α = 90
b = 80.93	β = 93.63
c = 110.544	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Eswaramoorthy, S., Mahmood, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary