1K0Z | pdb_00001k0z

Crystal Structure of the PvuII endonuclease with Pr3+ and SO4 ions bound in the active site at 2.05A.

• PDB DOI: https://doi.org/10.2210/pdb1K0Z/pdb

• Classification: HYDROLASE
• Organism(s): Proteus vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-21 Released: 2003-06-17 
• Deposition Author(s): Spyridaki, A., Athanasiadis, A., Matzen, C., Lanio, T., Jeltsch, A., Simoncsits, A., Scheuring-Vanamee, E., Kokkinidis, M., Pingoud, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.236 (Depositor) 
• R-Value Work: 
  0.190 (Depositor) 

Starting Model: experimental

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: 36.95 kDa 
• Atom Count: 2,722 
• Modeled Residue Count: 305 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II restriction enzyme PvuII	A, B	156	Proteus vulgaris	Mutation(s): 0  Gene Names: PvuiiR EC: 3.1.21.4
UniProt
Find proteins for P23657 (Proteus hauseri) Explore P23657  Go to UniProtKB:  P23657

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PR	C [auth A], E [auth B]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.236 (Depositor) 
• R-Value Work:  0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.74	α = 90
b = 105.63	β = 90
c = 46.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALA	data scaling
XTALVIEW	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-17 
Deposition Author(s): Spyridaki, A., Athanasiadis, A., Matzen, C., Lanio, T., Jeltsch, A., Simoncsits, A., Scheuring-Vanamee, E., Kokkinidis, M., Pingoud, A.

Revision History  

• Version 1.0: 2003-06-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description