4DIF | pdb_00004dif

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.224 (Depositor), 0.221 (DCC)
R-Value Work:
0.198 (Depositor), 0.196 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93NW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.224 (Depositor), 0.221 (DCC)
R-Value Work: 0.198 (Depositor), 0.196 (DCC)
R-Value Observed: 0.200 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Keatinge-Clay, A.T.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.