5M4B | pdb_00005m4b

Alpha-amino epsilon-caprolactam racemase D210A mutant in complex with PLP and geminal diamine intermediate

• PDB DOI: https://doi.org/10.2210/pdb5M4B/pdb

• Classification: ISOMERASE
• Organism(s): Rhizobacter
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-10-18 Released: 2017-04-19 
• Deposition Author(s): Frese, A., Sutton, P.W., Turkenburg, J.P., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.168 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Snapshots of the Catalytic Cycle of the Industrial Enzyme alpha-Amino-epsilon-Caprolactam Racemase (ACLR) Observed Using X-ray Crystallography

Frese, A., Sutton, P.W., Turkenburg, J.P., Grogan, G.

(2017) ACS Catal 7: 1045-1048

• DOI: https://doi.org/10.1021/acscatal.6b03056

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: 46.42 kDa 
• Atom Count: 3,588 
• Modeled Residue Count: 439 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class-III	A	440	Rhizobacter	Mutation(s): 1  Gene Names: RHSP_08934 EC: 5.1.1.15
UniProt
Find proteins for N6UXY4 (Rhizobium freirei PRF 81) Explore N6UXY4  Go to UniProtKB:  N6UXY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7F7	B [auth A]	[6-methyl-5-oxidanyl-4-[(~{E})-[(3~{R})-2-oxidanylideneazepan-3-yl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate C14 H20 N3 O6 P QOFJUFQRGNVZPX-KOSUEXCASA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.168 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.21	α = 90
b = 79.111	β = 112.82
c = 58.971	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Frese, A., Sutton, P.W., Turkenburg, J.P., Grogan, G.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary