3E9Q | pdb_00003e9q

Crystal Structure of the Short Chain Dehydrogenase from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb3E9Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shigella flexneri 2a str. 301
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-23 Released: 2008-09-23 
• Deposition Author(s): Kim, Y., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal Structure of the Short Chain Dehydrogenase from Shigella flexneri

Kim, Y., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A.

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: 62.66 kDa 
• Atom Count: 4,729 
• Modeled Residue Count: 511 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase	A, B	273	Shigella flexneri 2a str. 301	Mutation(s): 0  Gene Names: yciK, S1358, SF1273 EC: 1
UniProt
Find proteins for P31808 (Escherichia coli (strain K12)) Explore P31808  Go to UniProtKB:  P31808

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.08	α = 90
b = 133.2	β = 104.03
c = 48.232	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
RESOLVE	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-23 
Deposition Author(s): Kim, Y., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary