6DLI | pdb_00006dli

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

• PDB DOI: https://doi.org/10.2210/pdb6DLI/pdb

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


• Deposited: 2018-06-01 Released: 2019-06-05 
• Deposition Author(s): Cooling, G.T., Vance, N.R., Spies, M.A.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.244 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 120.6 kDa 
• Atom Count: 7,650 
• Modeled Residue Count: 1,024 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2N	E [auth A], G [auth B], H [auth C], J [auth D]	3-chloro-D-alanine C3 H6 Cl N O2 ASBJGPTTYPEMLP-UWTATZPHSA-N
GOL	F [auth A], I [auth C], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.244 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.888	α = 90
b = 95.605	β = 90
c = 179.284	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Cooling, G.T., Vance, N.R., Spies, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01 GM097373

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description