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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.267 (Depositor), 0.261 (DCC)
R-Value Work:
0.218 (Depositor), 0.215 (DCC)
R-Value Observed:
0.221 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure Analysis of Entamoeba histolytica Methyltransferase

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6Q386
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.267 (Depositor), 0.261 (DCC)
R-Value Work: 0.218 (Depositor), 0.215 (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

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Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.