5FJO

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

PDB DOI: https://doi.org/10.2210/pdb5FJO/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.175
R-Value Work: 0.145
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 79.61 kDa
Atom Count: 6,463
Modelled Residue Count: 735
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-succinylamino acid racemase	A, B	368	Amycolatopsis sp.	Mutation(s): 2 Gene Names: Aaar EC: 5.1.1 (PDB Primary Data), 4.2.1.113 (PDB Primary Data)
UniProt
Find proteins for Q44244 (Amycolatopsis sp) Explore Q44244 Go to UniProtKB: Q44244
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q44244
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NPQ Query on NPQ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	N-acetyl naphthylalanine C₁₅ H₁₅ N O₃ HGTIILKZSFKZMS-AWEZNQCLSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.175
R-Value Work: 0.145
R-Value Observed: 0.146
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.71	α = 90
b = 164.71	β = 90
c = 169.59	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-16

Deposition Author(s):

Sanchez-Carron, G.

Campopiano, D.

Grogan, G.

Revision History (Full details and data files)

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, Source and taxonomy, Structure summary

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Help and Resources

5FJO

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)