4XJX | pdb_00004xjx

STRUCTURE OF MUTANT (E165H) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

• PDB DOI: https://doi.org/10.2210/pdb4XJX/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-01-09 Released: 2016-01-20 
• Deposition Author(s): Baikova, T., Stsiapanava, A., Moche, M., Degtjarik, O., Kuta-Smatanova, I., Ettrich, R.
• Funding Organization(s): Czech Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

STRUCTURE OF MUTANT (E165H) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

Baikova, T., Ettrich, R.

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: 241.64 kDa 
• Atom Count: 14,686 
• Modeled Residue Count: 1,724 
• Deposited Residue Count: 2,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HsdR	A, B	1,038	Escherichia coli	Mutation(s): 1  Gene Names: hsdR EC: 3.1.21.3
UniProt
Find proteins for P10486 (Escherichia coli) Explore P10486  Go to UniProtKB:  P10486

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], F [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.243 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.221	α = 90
b = 124.542	β = 107.77
c = 128.54	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Baikova, T., Stsiapanava, A., Moche, M., Degtjarik, O., Kuta-Smatanova, I., Ettrich, R.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	P207/12/2323

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description