3GVI | pdb_00003gvi

Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb3GVI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-31 Released: 2009-04-14 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP

Abendroth, J., Staker, B.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 206.79 kDa 
• Atom Count: 15,183 
• Modeled Residue Count: 1,883 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D, E, F	324	Brucella abortus 2308	Mutation(s): 0  Gene Names: mdh, BAB1_1927 EC: 1.1.1.37
UniProt
Find proteins for Q2YLR9 (Brucella abortus (strain 2308)) Explore Q2YLR9  Go to UniProtKB:  Q2YLR9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GVI

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.39	α = 90
b = 193.9	β = 90
c = 102.68	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description