3GEM | pdb_00003gem

Crystal structure of short-chain dehydrogenase from Pseudomonas syringae

• PDB DOI: https://doi.org/10.2210/pdb3GEM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas savastanoi pv. phaseolicola 1448A
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-25 Released: 2009-03-10 
• Deposition Author(s): Osipiuk, J., Xu, X., Cui, H., Nocek, B., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

X-ray crystal structure of short-chain dehydrogenase from Pseudomonas syringae.

Osipiuk, J., Xu, X., Cui, H., Nocek, B., Savchenko, A., Edwards, A.M., Joachimiak, A.

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: 114.15 kDa 
• Atom Count: 7,638 
• Modeled Residue Count: 876 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D	260	Pseudomonas savastanoi pv. phaseolicola 1448A	Mutation(s): 0  Gene Names: PSPPH_1072 EC: 1.5.1.3 (UniProt), 1.5.1.50 (UniProt)
UniProt
Find proteins for Q48MN0 (Pseudomonas savastanoi pv. phaseolicola (strain 1448A / Race 6)) Explore Q48MN0  Go to UniProtKB:  Q48MN0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.83 Å
• R-Value Free:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.198	α = 90
b = 73.77	β = 90
c = 162.168	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Osipiuk, J., Xu, X., Cui, H., Nocek, B., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary