3I0P | pdb_00003i0p

Crystal structure of malate dehydrogenase from Entamoeba histolytica

• PDB DOI: https://doi.org/10.2210/pdb3I0P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-25 Released: 2009-07-14 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of malate dehydrogenase from Entamoeba histolytica

Edwards, T.E., Abendroth, J., Staker, B.L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Macromolecule Content 

• Total Structure Weight: 41.25 kDa 
• Atom Count: 2,950 
• Modeled Residue Count: 361 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A	365	Entamoeba histolytica	Mutation(s): 0
UniProt
Find proteins for C4M213 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4M213  Go to UniProtKB:  C4M213

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.232 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.23	α = 90
b = 106.23	β = 90
c = 72.114	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-07-14
  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: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description