3QV2 | pdb_00003qv2

Structure Analysis of Entamoeba histolytica methyltransferase EhMeth

• PDB DOI: https://doi.org/10.2210/pdb3QV2/pdb

• Classification: TRANSFERASE
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-25 Released: 2012-04-11 
• Deposition Author(s): Schulz, E.C., Roth, H.M., Ankri, S., Ficner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal Structure Analysis of Entamoeba histolytica Methyltransferase

Schulz, E.C., Roth, H.M., Ankri, S., Ficner, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 38.55 kDa 
• Atom Count: 2,886 
• Modeled Residue Count: 320 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-cytosine DNA methyltransferase	A	327	Entamoeba histolytica	Mutation(s): 0  Gene Names: meth, EHI_069140 EC: 2.1.1.37
UniProt
Find proteins for Q6Q386 (Entamoeba histolytica) Explore Q6Q386  Go to UniProtKB:  Q6Q386

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.97	α = 90
b = 46.97	β = 90
c = 303.24	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Schulz, E.C., Roth, H.M., Ankri, S., Ficner, R.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references, Derived calculations