3OUT | pdb_00003out

Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.

PDB DOI: https://doi.org/10.2210/pdb3OUT/pdb

Classification: ISOMERASE
Organism(s): Francisella tularensis subsp. tularensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-15 Released: 2010-09-29
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Kudriska, M., Edwards, A., Savchenko, A., Anderson, F.W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.193 (Depositor), 0.202 (DCC)
R-Value Work:
0.163 (Depositor), 0.174 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of glutamate racemase from Francisella tularensis subsp. tularensis SCHU S4 in complex with D-glutamate.

Filippova, E.V., Wawrzak, Z., Onopriyenko, O., Kudriska, M., Edwards, A., Savchenko, A., Anderson, F.W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 90.26 kDa
Atom Count: 6,958
Modeled Residue Count: 791
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate racemase	A, B, C	268	Francisella tularensis subsp. tularensis	Mutation(s): 0 Gene Names: FTT_1197c, murI EC: 5.1.1.3
UniProt
Find proteins for Q5NFN6 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFN6 Go to UniProtKB: Q5NFN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NFN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGL Query on DGL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	D [auth A], E [auth B], F [auth C]	D-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-GSVOUGTGSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.193 (Depositor), 0.202 (DCC)
R-Value Work: 0.163 (Depositor), 0.174 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.06	α = 90
b = 98.06	β = 90
c = 154.15	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
MrBUMP	phasing
PHENIX	model building
REFMAC	refinement
XSCALE	data scaling
CCP4	phasing
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Filippova, E.V.

Onopriyenko, O.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.