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- PDB-2pvi: PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA -

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Basic information

Entry
Database: PDB / ID: 2pvi
TitlePVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA
Components
  • DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3')
  • TYPE II RESTRICTION ENZYME PVUII
KeywordsHYDROLASE/DNA / COMPLEX (RESTRICTION ENDONUCLEASE-DNA) / HYDROLASE-DNA COMPLEX
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
DNA / DNA (> 10) / Type II restriction enzyme PvuII
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHorton, J. / Cheng, X.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
Authors: Horton, J.R. / Bonventre, J. / Cheng, X.
#1: Journal: Proteins / Year: 1994
Title: Expression, Purification, and Crystallization of Restriction Endonuclease PvuII with DNA Containing its Recognition Site
Authors: Balendiran, K. / Bonventre, J. / Knott, R. / Jack, W. / Benner, J. / Schildkraut, I. / Anderson, J.E.
#2: Journal: Embo J. / Year: 1994
Title: Structure of PvuII Endonuclease with Cognate DNA
Authors: Cheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E.
History
DepositionNov 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 20, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3')
D: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3')
A: TYPE II RESTRICTION ENZYME PVUII
B: TYPE II RESTRICTION ENZYME PVUII


Theoretical massNumber of molelcules
Total (without water)44,6294
Polymers44,6294
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.800, 86.300, 48.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3')


Mass: 4093.481 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein TYPE II RESTRICTION ENZYME PVUII / E.C.3.1.21.4 / ENDONUCLEASE PVUII / R.PVUII


Mass: 18220.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Plasmid: PPR594 / Production host: Escherichia coli (E. coli) / Strain (production host): PR653
References: UniProt: P23657, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5 / Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.76→19.5 Å / % possible obs: 77.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.1
Reflection shellResolution: 1.76→1.84 Å / % possible all: 23.7

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PVI

1pvi


Resolution: 1.76→19.5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: TWO CONFORMATIONS EXIST FOR HIS A84 AND HIS B84.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2929 10 %RANDOM
Rwork0.188 ---
obs0.188 115233 77.3 %-
all-115233 --
Refinement stepCycle: LAST / Resolution: 1.76→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 528 2 166 3289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
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
LS refinement shellResolution: 1.76→1.84 Å / Total num. of bins used: 8 /
Rfactor% reflection
Rfree0.313 -
Rwork0.298 -
obs-23.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARRAM11.DNATOPH11.DNA

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