3OXK

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

• PDB DOI: https://doi.org/10.2210/pdb3OXK/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Entamoeba histolytica HM-1:IMSS
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-21 Released: 2010-10-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.208 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

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

• PubMed: 25945711 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

Seattle Structural Genomics Center for Infectious Disease, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 13.49 kDa 
• Atom Count: 1,125 
• Modelled Residue Count: 115 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative histidine triad family protein	A	117	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0  Gene Names: EHI_093910 EC: 3.9.1
UniProt
Find proteins for C4LYI2 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LYI2  Go to UniProtKB:  C4LYI2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	C [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EOH	D [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.208 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M33OXK

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.66	α = 90
b = 60.86	β = 90
c = 67.93	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-10-06
  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: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description