4WGH | pdb_00004wgh

Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4WGH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-09-18 Released: 2014-10-01 
• Deposition Author(s): Bacal, P., Shabalin, I.G., Cooper, D.R., Hillerich, B.S., Zimmerman, M.D., Chowdhury, S., Hammonds, J., Al Obaidi, N., Gizzi, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution

Bacal, P., Shabalin, I.G., Cooper, D.R., Hillerich, B.S., Zimmerman, M.D., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.57 kDa 
• Atom Count: 2,462 
• Modeled Residue Count: 283 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde reductase	A	306	Klebsiella pneumoniae	Mutation(s): 1  Gene Names: L364_03163, WP_004176538.1

Small Molecules

Ligands 2 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
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3C884

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.483	α = 90
b = 99.483	β = 90
c = 55.181	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
DM	phasing
MLPHARE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Bacal, P., Shabalin, I.G., Cooper, D.R., Hillerich, B.S., Zimmerman, M.D., Chowdhury, S., Hammonds, J., Al Obaidi, N., Gizzi, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM094662

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Data collection
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-10-16
  Changes: Structure summary