8TBA | pdb_00008tba

Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a crystallographic artifact

• PDB DOI: https://doi.org/10.2210/pdb8TBA/pdb

• Classification: ISOMERASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-28 Released: 2024-07-03 
• Deposition Author(s): Propp, J., Spies, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a likely crystallographic artifact

Propp, J., Spies, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 58.26 kDa 
• Atom Count: 4,274 
• Modeled Residue Count: 496 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate racemase	A, B	256	Helicobacter pylori	Mutation(s): 0  Gene Names: murI EC: 5.1.1.3
UniProt
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZLT0  Go to UniProtKB:  Q9ZLT0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZMX (Subject of Investigation/LOI)	C [auth A]	(2M)-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-2-[5-(4-methylphenyl)-1,3-oxazol-2-yl]benzamide C28 H24 N4 O3 MWAFTVRXNXVJSM-UHFFFAOYSA-N
DGL	D [auth A], F [auth B]	D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N
DMS	E [auth A], G [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DGL	BindingDB:  8TBA	Ki: 5800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.35	α = 90
b = 79.868	β = 90
c = 114.887	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Propp, J., Spies, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM138471-01

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release