3K5P

Crystal structure of amino acid-binding ACT: D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb3K5P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-10-07 Released: 2009-11-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of amino acid-binding ACT: D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain from Brucella melitensis

Edwards, T.E., Abendroth, J., Smith, E.R., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.37 kDa 
• Atom Count: 3,293 
• Modelled Residue Count: 400 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A	416	Brucella abortus 2308	Mutation(s): 1  Gene Names: BMEII0813 EC: 1.1.1.95
UniProt
Find proteins for Q2YK82 (Brucella abortus (strain 2308)) Explore Q2YK82  Go to UniProtKB:  Q2YK82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 6₂ 2 2
• Diffraction Data: https://doi.org/10.18430/M33K5P

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.891	α = 90
b = 97.891	β = 90
c = 189.215	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description