3IPW

Crystal structure of hydrolase TatD family protein from Entamoeba histolytica

• PDB DOI: https://doi.org/10.2210/pdb3IPW/pdb

• Classification: HYDROLASE
• Organism(s): Entamoeba histolytica HM-1:IMSS
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-18 Released: 2009-09-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Crystal structure of hydrolase TatD family protein from Entamoeba histolytica

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.6 kDa 
• Atom Count: 2,577 
• Modelled Residue Count: 301 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase TatD family protein	A	325	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0  Gene Names: EHI_119490
UniProt
Find proteins for C4M7X7 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4M7X7  Go to UniProtKB:  C4M7X7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.392	α = 90
b = 83.392	β = 90
c = 90.405	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-09-01
  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