4DIF

Structure of A1-type ketoreductase

• PDB DOI: https://doi.org/10.2210/pdb4DIF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces nodosus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-30 Released: 2013-02-13 
• Deposition Author(s): Zheng, J., Keatinge-Clay, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.224 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Structure and mutagenesis of A2-type ketoreductase from modular polyketide synthase reveals insights into stereospecificity

Zheng, J., Keatinge-Clay, A.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.54 kDa 
• Atom Count: 7,653 
• Modelled Residue Count: 952 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmphB	A, B	496	Streptomyces nodosus	Mutation(s): 2  Gene Names: amphB EC: 1.1.1.100
UniProt
Find proteins for Q93NW7 (Streptomyces nodosus) Explore Q93NW7  Go to UniProtKB:  Q93NW7

Small Molecules

Ligands 2 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
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.224 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.546	α = 72.92
b = 63.716	β = 67.22
c = 71.983	γ = 89.74

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Zheng, J., Keatinge-Clay, A.T.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description