4E0B | pdb_00004e0b

2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6

• PDB DOI: https://doi.org/10.2210/pdb4E0B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-02 Released: 2012-03-21 
• Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.207 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6

Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.87 kDa 
• Atom Count: 9,771 
• Modeled Residue Count: 1,220 
• Deposited Residue Count: 1,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D	313	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: mdh, VV1_0673 EC: 1.1.1.37
UniProt
Find proteins for Q8DEC2 (Vibrio vulnificus (strain CMCP6)) Explore Q8DEC2  Go to UniProtKB:  Q8DEC2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth B], G [auth C], H [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.207 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34e0b

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.04	α = 90
b = 80.76	β = 109.42
c = 99.43	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
mrbump/molrep	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MRBUMP/MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary