3GZ4 | pdb_00003gz4

Crystal structure of putative short chain dehydrogenase FROM ESCHERICHIA COLI CFT073 complexed with NADPH

• PDB DOI: https://doi.org/10.2210/pdb3GZ4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli O6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-06 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: 2.10 Å
• R-Value Free: 
  0.252 (Depositor) 
• R-Value Work: 
  0.226 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of putative short chain dehydrogenase FROM ESCHERICHIA COLI CFT073 complexed with NADPH

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: 59.85 kDa 
• Atom Count: 3,959 
• Modeled Residue Count: 482 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical oxidoreductase yciK	A, B	262	Escherichia coli O6	Mutation(s): 0  Gene Names: AAN80202.1, c1736, yciK EC: 1
UniProt
Find proteins for A0A0H2V6Y9 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V6Y9  Go to UniProtKB:  A0A0H2V6Y9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.252 (Depositor) 
• R-Value Work:  0.226 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.794	α = 90
b = 130.511	β = 115.06
c = 47.934	γ = 90

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: 2013-12-04
  Changes: Non-polymer description
• Version 1.4: 2017-11-01
  Changes: Refinement description
• Version 1.5: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-02-21
  Changes: Data collection, Database references