3GY0 | pdb_00003gy0

Crystal structure of putatitve short chain dehydrogenase FROM SHIGELLA FLEXNERI 2A STR. 301 complexed with NADP

• PDB DOI: https://doi.org/10.2210/pdb3GY0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-03 Released: 2009-04-14 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.193 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of putatitve short chain dehydrogenase FROM SHIGELLA FLEXNERI 2A STR. 301 complexed with NADP

Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 29.11 kDa 
• Atom Count: 2,198 
• Modeled Residue Count: 239 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dehydrogenase	A	255	Shigella flexneri	Mutation(s): 0  Gene Names: yciK, S1358, SF1273
UniProt
Find proteins for A0A0H2UYY2 (Shigella flexneri) Explore A0A0H2UYY2  Go to UniProtKB:  A0A0H2UYY2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.193 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.819	α = 90
b = 88.819	β = 90
c = 80.505	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2012-10-24
  Changes: Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-11-21
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references