6W04 | pdb_00006w04

Crystal structure of HAD hydrolase, family IA, variant 3 from Entamoeba histolytica HM-1:IMSS

PDB DOI: https://doi.org/10.2210/pdb6W04/pdb

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

Deposited: 2020-02-29 Released: 2020-03-18
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.158 (Depositor), 0.161 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6W04

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

Literature

Crystal structure of HAD hydrolase, family IA, variant 3 from Entamoeba histolytica HM-1:IMSS

Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 26.56 kDa
Atom Count: 1,961
Modeled Residue Count: 223
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HAD hydrolase, family IA, variant 3	A	231	Entamoeba histolytica	Mutation(s): 0 Gene Names: EHI_073350 EC: 3
UniProt
Find proteins for C4LXK0 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LXK0 Go to UniProtKB: C4LXK0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4LXK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.158 (Depositor), 0.161 (DCC)
R-Value Observed: 0.163 (Depositor)

Diffraction Data:

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.91	α = 90
b = 100.91	β = 90
c = 45.24	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2024-03-06
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.