4O0K

Crystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis with covalently bound substrate

PDB DOI: https://doi.org/10.2210/pdb4O0K/pdb

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

Deposited: 2013-12-13 Released: 2014-01-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.177
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis with covalently bound substrate

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

To be published.

Macromolecule Content

Total Structure Weight: 35.85 kDa
Atom Count: 2,959
Modelled Residue Count: 323
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthetase	A	329	Brucella melitensis ATCC 23457	Mutation(s): 0 Gene Names: 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI Query on KPI	A	L-PEPTIDE LINKING	C₉ H₁₆ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.177
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 6₃ 2 2
Diffraction Data: https://doi.org/10.18430/M34O0K

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.28	α = 90
b = 95.28	β = 90
c = 125.25	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-29
Changes: Data collection

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Help and Resources

4O0K

Crystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis with covalently bound substrate

Crystal structure of 1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis with covalently bound substrate

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)