2PWZ | pdb_00002pwz

Crystal structure of the apo form of E.Coli malate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb2PWZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2007-05-14 Released: 2007-05-29 
• Deposition Author(s): Soderberg, C.A.G., Clarke, T.A., Richardson, D.J., Hemmings, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

The X-ray crystal structure of the apo form of E.Coli malate dehydrogenase in space group C2

Soderberg, C.A.G., Clarke, T.A., Richardson, D.J., Hemmings, A.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 129.47 kDa 
• Atom Count: 9,470 
• Modeled Residue Count: 1,244 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B [auth C], C [auth E], D [auth G]	312	Escherichia coli K-12	Mutation(s): 0  EC: 1.1.1.37
UniProt
Find proteins for P61889 (Escherichia coli (strain K12)) Explore P61889  Go to UniProtKB:  P61889

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.466	α = 90
b = 52.485	β = 102.28
c = 170.2	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Soderberg, C.A.G., Clarke, T.A., Richardson, D.J., Hemmings, A.M.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description