3HFR

Crystal structure of glutamate racemase from Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb3HFR/pdb

Classification: ISOMERASE
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-12 Released: 2009-06-09
Deposition Author(s): Majorek, K.A., Chruszcz, M., Zimmerman, M.D., Klimecka, M.M., Cymborowski, M., Skarina, T., Onopriyenko, O., Stam, J., Otwinowski, Z., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of glutamate racemase from Listeria monocytogenes

Majorek, K.A., Chruszcz, M., Zimmerman, M.D., Klimecka, M.M., Cymborowski, M., Skarina, T., Onopriyenko, O., Stam, J., Otwinowski, Z., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 61.49 kDa
Atom Count: 4,381
Modelled Residue Count: 532
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate racemase	A, B	269	Listeria monocytogenes	Mutation(s): 0 Gene Names: lmo1237, murI, racE EC: 5.1.1.3
UniProt
Find proteins for Q8Y7N7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y7N7 Go to UniProtKB: Q8Y7N7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y7N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JEF Query on JEF Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B]	E [auth A], F [auth A], H [auth B]	O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) C₃₀ H₆₃ N O₁₀ ICCXIDTYQFYPNV-RUMGZKRTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	C [auth A], D [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.244
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: P 4₃ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M3PK5W

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.651	α = 90
b = 66.651	β = 90
c = 257.99	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
CCP4	model building
O	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2018-10-03
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2022-04-13
Changes: Database references, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3HFR

Crystal structure of glutamate racemase from Listeria monocytogenes

Crystal structure of glutamate racemase from Listeria monocytogenes

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)