4MPQ | pdb_00004mpq

Crystal structure of1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis ATCC 23457

PDB DOI: https://doi.org/10.2210/pdb4MPQ/pdb

Classification: LYASE
Organism(s): Brucella melitensis ATCC 23457
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-13 Released: 2013-09-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.185 (Depositor), 0.190 (DCC)
R-Value Work:
0.159 (Depositor), 0.170 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis ATCC 23457

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lukacz, C., Lorimer, D., Edwards, T.

To be published.

Macromolecule Content

Total Structure Weight: 35.72 kDa
Atom Count: 2,880
Modeled Residue Count: 324
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthetase	A	329	Brucella melitensis ATCC 23457	Mutation(s): 0 Gene Names: BM28_B0232, BMEA_B0240 EC: 3.5.4.22
UniProt
Find proteins for C0RKH4 (Brucella melitensis biotype 2 (strain ATCC 23457)) Explore C0RKH4 Go to UniProtKB: C0RKH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0RKH4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.185 (Depositor), 0.190 (DCC)
R-Value Work: 0.159 (Depositor), 0.170 (DCC)
R-Value Observed: 0.160 (Depositor)

Diffraction Data:

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.06	α = 90
b = 95.06	β = 90
c = 125.33	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-09-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-09-25
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.