7L9R | pdb_00007l9r

Crystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica

• PDB DOI: https://doi.org/10.2210/pdb7L9R/pdb

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


• Deposited: 2021-01-04 Released: 2021-02-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica

Abendroth, J., Davies, D.R., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 79.17 kDa 
• Atom Count: 4,537 
• Modeled Residue Count: 562 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyhypusine synthase, putative	A, B	352	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0  Gene Names: EHI_098350
UniProt
Find proteins for C4LXB8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LXB8  Go to UniProtKB:  C4LXB8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37l9r

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.9	α = 90
b = 85.9	β = 90
c = 424.52	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
BUCCANEER	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description