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- PDB-1pvi: STRUCTURE OF PVUII ENDONUCLEASE WITH COGNATE DNA -

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Basic information

Entry
Database: PDB / ID: 1pvi
TitleSTRUCTURE OF PVUII ENDONUCLEASE WITH COGNATE DNA
Components
  • DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
  • PROTEIN (PVUII (E.C.3.1.21.4))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / 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 / Resolution: 2.6 Å
AuthorsCheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E.
Citation
Journal: EMBO J. / Year: 1994
Title: Structure of PvuII endonuclease with cognate DNA.
Authors: Cheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E.
#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.
History
DepositionNov 16, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
C: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
D: DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
A: PROTEIN (PVUII (E.C.3.1.21.4))
B: PROTEIN (PVUII (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)44,6774
Polymers44,6774
Non-polymers00
Water00
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
Space group name H-MP212121

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Components

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


Mass: 3967.585 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (PVUII (E.C.3.1.21.4))


Mass: 18370.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Proteus vulgaris (bacteria) / References: UniProt: P23657

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal grow
*PLUS
Temperature: 16 K / pH: 4.5 / Method: vapor diffusion, hanging drop
Details: Balendiran, K., (1994) Proteins: Struct.,Funct., Genet., 19, 77.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.6 mg/mlR-PvuII1drop
21.6 mg/mlduplex DNA1drop
318-25 %mother liquor1drop
48 %PEG40001dropmother liquor
50.3 mMEDTA1dropmother liquor
650 mMsodium acetate1drop
731-45 %mother liquor1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 4.4 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Num. obs: 10282 / % possible obs: 92.7 % / Redundancy: 4.4 % / Num. measured all: 45607 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORrefinement
MADNESdata reduction
RefinementResolution: 2.6→10 Å
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 9799 92.7 %
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 526 0 0 3196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.7
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / Total num. of bins used: 5

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