6H2J

Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2W00 - determined by Lapkouski, M., Panjikar, S., Kuta Smatanova, I., Ettrich, R., Csefalvay, E.  
  • 5J3N - determined by Grinkevich, P., Iermak, I., Luedtke, N., Mesters, J.R., Ettrich, R., Ludwig, J.  

Literature

Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.

Grinkevich, P.Sinha, D.Iermak, I.Guzanova, A.Weiserova, M.Ludwig, J.Mesters, J.R.Ettrich, R.H.

(2018) J. Biol. Chem. 293: 15043-15054


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type I restriction enzyme R Protein
A, B
1038Escherichia coliMutation(s): 0 
Gene Names: hsdR (hsr)
EC: 3.1.21.3
Find proteins for P10486 (Escherichia coli)
Go to UniProtKB:  P10486
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 123.910α = 90.00
b = 129.922β = 90.00
c = 161.010γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
Auto-Rickshawphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicP207/12/2323

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references