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), 0.220 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Z [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	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 M [auth B] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [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 Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth D] 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), 0.220 (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

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