3E03 | pdb_00003e03

Crystal structure of a putative dehydrogenase from Xanthomonas campestris

• PDB DOI: https://doi.org/10.2210/pdb3E03/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-30 Released: 2008-09-16 
• Deposition Author(s): Sampathkumar, P., Wasserman, S., Rutter, M., Hu, S., Bain, K., Rodgers, L., Atwell, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.199 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Crystal structure of a putative dehydrogenase from Xanthomonas campestris

Sampathkumar, P., Wasserman, S., Rutter, M., Hu, S., Bain, K., Rodgers, L., Atwell, S., Sauder, J.M., Burley, S.K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 86.1 kDa 
• Atom Count: 6,748 
• Modeled Residue Count: 810 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C	274	Xanthomonas campestris pv. campestris	Mutation(s): 0  Gene Names: XCC3285
UniProt
Find proteins for Q8P5Q1 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P5Q1  Go to UniProtKB:  Q8P5Q1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.199 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 251.286	α = 90
b = 41.351	β = 96.62
c = 73.323	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Sampathkumar, P., Wasserman, S., Rutter, M., Hu, S., Bain, K., Rodgers, L., Atwell, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary