3IAH

Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.

• PDB DOI: https://doi.org/10.2210/pdb3IAH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-14 Released: 2009-07-21 
• Deposition Author(s): Minasov, G., Halavaty, A., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.176 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Literature

Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.

Minasov, G., Halavaty, A., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 59.48 kDa 
• Atom Count: 4,689 
• Modelled Residue Count: 505 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short Chain Dehydrogenase yciK	A, B	256	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: STM1717, yciK
UniProt
Find proteins for Q7CQG2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CQG2  Go to UniProtKB:  Q7CQG2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], I [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ACT	D [auth A], E [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
EOH	F [auth A], G [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.83 Å
• R-Value Free: 0.176 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M33IAH

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.664	α = 90
b = 43.302	β = 93.24
c = 71.916	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Minasov, G., Halavaty, A., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection