5FJP | pdb_00005fjp

N-acyl amino acid racemase from Amycolatopsis sp Ts-1-60: G291D F323Y I293G mutant in complex with N-acetyl naphthylalanine

• PDB DOI: https://doi.org/10.2210/pdb5FJP/pdb

• Classification: LYASE
• Organism(s): Amycolatopsis sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-10-12 Released: 2016-11-16 
• Deposition Author(s): Sanchez Carron, G., Campopiano, D., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of N-Acylamino Acid Racemase Mutants in Complex with Substrates

Sanchez-Carron, G., Campopiano, D., Grogan, G.

To be published.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 158.99 kDa 
• Atom Count: 11,378 
• Modeled Residue Count: 1,470 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-SUCCINYLBENZOATE SYNTHASE	A, B, C, D	368	Amycolatopsis sp.	Mutation(s): 3  EC: 4.2.1.113 (PDB Primary Data), 5.1.1 (UniProt)
UniProt
Find proteins for Q44244 (Amycolatopsis sp) Explore Q44244  Go to UniProtKB:  Q44244

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPQ	E [auth A], G [auth B], I [auth C], K [auth D]	N-acetyl naphthylalanine C15 H15 N O3 HGTIILKZSFKZMS-AWEZNQCLSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.29	α = 90
b = 217.29	β = 90
c = 262.22	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Sanchez Carron, G., Campopiano, D., Grogan, G.

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description