2AR0

Crystal structure of Type I restriction enzyme EcoKI M protein (EC 2.1.1.72) (M.EcoKI)

• PDB DOI: https://doi.org/10.2210/pdb2AR0/pdb

• Classification: TRANSCRIPTION,TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-08-18 Released: 2005-08-30 
• Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.261 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Crystal structure of Type I restriction enzyme EcoKI M protein (EC 2.1.1.72) (M.EcoKI).

Rajashankar, K.R., Kniewel, R., Lima, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 122.51 kDa 
• Atom Count: 7,828 
• Modelled Residue Count: 968 
• Deposited Residue Count: 1,082 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I restriction enzyme EcoKI M protein	A, B	541	Escherichia coli	Mutation(s): 10  Gene Names: hsdM, hsm EC: 2.1.1.72
UniProt
Find proteins for P08957 (Escherichia coli (strain K12)) Explore P08957  Go to UniProtKB:  P08957

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.261 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.427	α = 90
b = 105.427	β = 90
c = 138.279	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-30 
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-08-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Refinement description