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- PDB-1eyu: HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA C... -

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Basic information

Entry
Database: PDB / ID: 1eyu
TitleHIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6
Components
  • DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
  • TYPE II RESTRICTION ENZYME PVUII
Keywordshydrolase/DNA / PROTEIN-DNA COMPLEX / endonuclease type II / restriction enzyme / 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: 1.78 Å
AuthorsHorton, J.R. / Cheng, X.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: PvuII endonuclease contains two calcium ions in active sites.
Authors: Horton, J.R. / Cheng, X.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Asp34 of PvuII Endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis
Authors: Horton, J.R. / Nastri, H.G. / Riggs, P.D. / Cheng, X.
#2: Journal: 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.
History
DepositionMay 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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: TYPE II RESTRICTION ENZYME PVUII
B: TYPE II RESTRICTION ENZYME PVUII


Theoretical massNumber of molelcules
Total (without water)44,6774
Polymers44,6774
Non-polymers00
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.797, 84.336, 46.155
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is the endonuclease dimer (chain A and chain B) and doubled-stranded oligonucleotide (chain C and chain D).

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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
Details: SELF-ANNEALING OLIGONUCLEOTIDE CONTAINING COGNATE SIX BASE PAIR SEQUENCE
#2: Protein TYPE II RESTRICTION ENZYME PVUII / E.C.3.1.21.4 / PVUII ENDONUCLEASE / R.PVUII


Mass: 18370.992 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)
References: UniProt: P23657, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 4000, sodium acetate, CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2CaCl211
3PEG 400011
4PEG 400012
Crystal grow
*PLUS
Temperature: 16 ℃
Details: Balendiran, K., (1994) Proteins: Struct. Funct. Genet., 19, 77.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19.6 mg/mlprotein1drop
21.6 mg/mlduplex DNA1drop
325 mM1dropCaCl2
418-25 %PEG40001dropmother liquor
50.3 mMEDTA1dropmother liquor
650 mMsodium acetate1dropmother liquor
731-45 %mother liquor1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. all: 35254 / Num. obs: 35254 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 3621.7
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.198 / Num. unique all: 1686 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 130055
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.78→25 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3603 10.5 %RANDOM
Rwork0.208 ---
all0.237 34254 --
obs0.24 31651 97.9 %-
Refinement stepCycle: LAST / Resolution: 1.78→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 511 0 366 3400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_torsion_deg22.9
X-RAY DIFFRACTIONx_torsion_impr_deg1.23

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