5D2E | pdb_00005d2e

crystal structure of an N-terminal ketoreductase from macrolactin assembly line

• PDB DOI: https://doi.org/10.2210/pdb5D2E/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus velezensis FZB42
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-08-05 Released: 2015-08-26 
• Deposition Author(s): Keatinge-clay, A.T., Zeng, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of an N-terminal ketoreductase from macrolactin polyketide synthase

Zeng, 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)

Macromolecule Content 

• Total Structure Weight: 60.08 kDa 
• Atom Count: 4,294 
• Modeled Residue Count: 485 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MlnE	A	522	Bacillus velezensis FZB42	Mutation(s): 0  Gene Names: mlnE, RBAM_014370
UniProt
Find proteins for A7Z474 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)) Explore A7Z474  Go to UniProtKB:  A7Z474

Small Molecules

Ligands 3 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
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.627	α = 90
b = 110.933	β = 90
c = 139.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Keatinge-clay, A.T., Zeng, J.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description