4O0K | pdb_00004o0k

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34O0K

Space Group: P 6₃ 2 2

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

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• 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