1NI0 | pdb_00001ni0

Structure of the Y94F mutant of the restriction endonuclease PvuII

• PDB DOI: https://doi.org/10.2210/pdb1NI0/pdb

• Classification: HYDROLASE
• Organism(s): Proteus vulgaris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-12-20 Released: 2003-02-04 
• Deposition Author(s): Tucker, P.A., Kokkinidis, M., Nicolaki, S., Kotsifaki, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.290 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Structure of the Y94F mutant of the restriction endonuclease PvuII

Tucker, P.A., Kokkinidis, M., Nicolaki, S., Kotsifaki, D.

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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.49 kDa 
• Atom Count: 4,078 
• Modeled Residue Count: 472 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II restriction enzyme PvuII	A, B, C	159	Proteus vulgaris	Mutation(s): 1  Gene Names: PVUIIR EC: 3.1.21.4
UniProt
Find proteins for P23657 (Proteus hauseri) Explore P23657  Go to UniProtKB:  P23657

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.290 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.86	α = 90
b = 176.86	β = 90
c = 46.34	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-04 
Deposition Author(s): Tucker, P.A., Kokkinidis, M., Nicolaki, S., Kotsifaki, D.

Revision History  

• Version 1.0: 2003-02-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Data collection, Database references
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description