4Q04 | pdb_00004q04

Crystal structure of URE3-BP from Entomaeba histolytica without calcium

• PDB DOI: https://doi.org/10.2210/pdb4Q04/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Entamoeba histolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2014-04-23 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of URE3-BP from Entomaeba histolytica

Edwards, T.E., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease

To be published.

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: 51.79 kDa 
• Atom Count: 3,779 
• Modeled Residue Count: 426 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URE3-BP sequence specific DNA binding protein	A, B	220	Entamoeba histolytica	Mutation(s): 0  Gene Names: URE3-BP
UniProt
Find proteins for Q9GSV7 (Entamoeba histolytica) Explore Q9GSV7  Go to UniProtKB:  Q9GSV7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34Q04

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.42	α = 90
b = 69.42	β = 90
c = 187.36	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description