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- PDB-1f0o: PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKE... -

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Basic information

Entry
Database: PDB / ID: 1f0o
TitlePVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE
Components
  • (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 / Catalytic Metal visualization / 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: 2.5 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 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C-3')
D: (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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8378
Polymers44,6774
Non-polymers1604
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.043, 84.702, 45.993
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a dimer consisting of protein chain A and chain B and double strained DNA consisting of chains C and D with two CA+2 at each monomeric active site.

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Components

#1: DNA chain (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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 39.55 %
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-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

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 13150 / Num. obs: 13150 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.332 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 61937

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1241 10 %RANDOM
Rwork0.205 ---
all0.205 12739 --
obs0.279 12739 96 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 511 4 190 3154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.2
X-RAY DIFFRACTIONx_torsion_impr_deg1.37
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.3

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