5W16 | pdb_00005w16

Crystal structure of glutamate racemase from Thermus thermophilus in complex with D-glutamate

PDB DOI: https://doi.org/10.2210/pdb5W16/pdb

Classification: ISOMERASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-06-01 Released: 2018-06-06
Deposition Author(s): Cooling, G.T., Vance, N.R., Spies, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.225 (Depositor), 0.225 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of glutamate racemase from Thermus Thermophilus in complex with D-glutamate

Cooling, G.T., Vance, N.R., Spies, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 121.7 kDa
Atom Count: 8,682
Modeled Residue Count: 1,024
Deposited Residue Count: 1,112
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate racemase	A, B, C, D	278	Thermus thermophilus	Mutation(s): 0 Gene Names: murI, TTHA1643 EC: 5.1.1.3
UniProt
Find proteins for Q5SHT7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHT7 Go to UniProtKB: Q5SHT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGL Query on DGL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain Z [auth D]	E [auth A], L [auth B], Q [auth C], Z [auth D]	D-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-GSVOUGTGSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain Z [auth D]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] F [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain W [auth C] SDF format, chain O [auth B] SDF format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth C] MOL2 format, chain O [auth B] MOL2 format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth C] mmCIF format, chain O [auth B] mmCIF format, chain EA [auth D]	EA [auth D] FA [auth D] K [auth A] O [auth B] P [auth B] EA [auth D], FA [auth D], K [auth A], O [auth B], P [auth B], W [auth C], X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.225 (Depositor), 0.225 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.677	α = 90
b = 96.728	β = 90
c = 179.066	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

Cooling, G.T.

Vance, N.R.

Spies, M.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM097373

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description