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- PDB-1pvu: THE CRYSTAL STRUCTURE OF PVUII ENDONUCLEASE REVEALS EXTENSIVE STR... -

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Basic information

Entry
Database: PDB / ID: 1pvu
TitleTHE CRYSTAL STRUCTURE OF PVUII ENDONUCLEASE REVEALS EXTENSIVE STRUCTURAL HOMOLOGIES TO ECORV
ComponentsPvu II
KeywordsTYPE II RESTRICTION ENDONUCLEASE
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
PVUII Endonuclease, subunit A / Restriction endonuclease, type II, PvuII / Restriction endonuclease, type II, PvuII superfamily / Restriction endonuclease PvuII / PvuII Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II restriction enzyme PvuII
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsVlassi, M. / Athanasiadis, A.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.
Authors: Athanasiadis, A. / Vlassi, M. / Kotsifaki, D. / Tucker, P.A. / Wilson, K.S. / Kokkinidis, M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Purification,Crystallization and Preliminary X-Ray Diffraction Studies of the PvuII Endonuclease
Authors: Athanasiadis, A. / Kokkinidis, M.
#2: Journal: Nucleic Acids Res. / Year: 1990
Title: Complete Nucleotide Sequence of the PvuII Restriction Enzyme Gene from Proteus Vulgaris
Authors: Athanasiadis, A. / Gregoriu, M. / Thanos, D. / Kokkinidis, M. / Papamatheakis, J.
History
DepositionMar 9, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pvu II
B: Pvu II


Theoretical massNumber of molelcules
Total (without water)36,4802
Polymers36,4802
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-21 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.650, 106.460, 47.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.732901, -0.680335, -0.000615), (-0.680161, -0.732733, 0.021998), (-0.015417, -0.015704, -0.999758)
Vector: 40.796, 102.794, 36.961)

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Components

#1: Protein Pvu II


Mass: 18239.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria)
References: UniProt: P23657, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5 / Method: vapor diffusion, hanging drop / Details: Athanasiadis, A., (1991) J.Mol.Biol., 222, 451.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein solution1drop
2100 mMammonium acetate1drop
310-20 %ammonium sulfate1drop
444 %ammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 16315 / % possible obs: 96.3 % / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 15332
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 0 79 2623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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