5FJU | pdb_00005fju

N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl phenylalanine

PDB DOI: https://doi.org/10.2210/pdb5FJU/pdb

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

Deposited: 2015-10-13 Released: 2016-11-16
Deposition Author(s): Sanchez Carron, G., Campopiano, D., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.190 (Depositor), 0.197 (DCC)
R-Value Work:
0.156 (Depositor), 0.164 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 159.54 kDa
Atom Count: 11,561
Modeled Residue Count: 1,469
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-SUCCINYLBENZOATE SYNTHASE	A, B, C, D	368	Amycolatopsis sp.	Mutation(s): 4 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q44244
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5CR Query on 5CR Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	N-acetyl-L-phenylalanine C₁₁ H₁₃ N O₃ CBQJSKKFNMDLON-JTQLQIEISA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.190 (Depositor), 0.197 (DCC)
R-Value Work: 0.156 (Depositor), 0.164 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.9	α = 90
b = 216.9	β = 90
c = 261.63	γ = 120

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

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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: 2017-09-13
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

5FJU | pdb_00005fju

N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl phenylalanine

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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