3OMF

Crystal structure of a histidine triad family protein from Entamoeba histolytica, bound to AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of a histidine triad family protein from Entamoeba histolytica bound to sulfate, AMP and GMP.

Lorimer, D.D.Choi, R.Abramov, A.Nakazawa Hewitt, S.Gardberg, A.S.Van Voorhis, W.C.Staker, B.L.Myler, P.J.Edwards, T.E.

(2015) Acta Crystallogr F Struct Biol Commun 71: 572-576

  • DOI: 10.1107/S2053230X1500237X
  • Primary Citation of Related Structures:  
    3OJ7, 3OMF, 3OXK

  • PubMed Abstract: 
  • Three structures of the histidine triad family protein from Entamoeba histolytica, the causative agent of amoebic dysentery, were solved at high resolution within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The structures ...

    Three structures of the histidine triad family protein from Entamoeba histolytica, the causative agent of amoebic dysentery, were solved at high resolution within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The structures have sulfate (PDB entry 3oj7), AMP (PDB entry 3omf) or GMP (PDB entry 3oxk) bound in the active site, with sulfate occupying the same space as the α-phosphate of the two nucleotides. The C(α) backbones of the three structures are nearly superimposable, with pairwise r.m.s.d.s ranging from 0.06 to 0.13 Å.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative histidine triad family proteinA117Entamoeba histolytica HM-1:IMSSMutation(s): 0 
Gene Names: EHI_093910
EC: 3
Find proteins for C4LYI2 (Entamoeba histolytica)
Explore C4LYI2 
Go to UniProtKB:  C4LYI2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.58α = 90
b = 60.63β = 90
c = 67.88γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-05-20
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary