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- PDB-1vas: ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYM... -

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Basic information

Entry
Database: PDB / ID: 1vas
TitleATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION
Components
  • DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')
  • PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


deoxyribodipyrimidine endonucleosidase / pyrimidine dimer DNA N-glycosylase activity / deoxyribodipyrimidine endonucleosidase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / endonuclease activity / DNA repair
Similarity search - Function
Endonuclease V / T4 endonuclease V / Pyrimidine dimer DNA glycosylase / Pyrimidine dimer DNA glycosylase, endonuclease V type / T4 endonuclease V / Pyrimidine dimer DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease V
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsVassylyev, D.G. / Kashiwagi, T. / Mikami, Y. / Ariyoshi, M. / Iwai, S. / Ohtsuka, E. / Morikawa, K.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
Authors: Vassylyev, D.G. / Kashiwagi, T. / Mikami, Y. / Ariyoshi, M. / Iwai, S. / Ohtsuka, E. / Morikawa, K.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal Structure of a Pyrimidine Dimer-Specific Excision Repair Enzyme from Bacteriophage T4: Refinement at 1.45 Angstroms and X-Ray Analysis of the Three Active Site Mutants
Authors: Morikawa, K. / Ariyoshi, M. / Vassylyev, D.G. / Matsumoto, O. / Katayanagi, K. / Ohtsuka, E.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1993
Title: DNA Repair Enzymes
Authors: Morikawa, K.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Role of the Basic Amino Acid Cluster and Glu-23 in Pyrimidine Dimer Glycosylase Activity of T4 Endonuclease V
Authors: Doi, T. / Recktenwald, A. / Karaki, Y. / Kikuchi, M. / Morikawa, K. / Ikehara, M. / Inaoka, T. / Hori, N. / Ohtsuka, E.
#4: Journal: Science / Year: 1992
Title: X-Ray Structure of T4 Endonuclease V: An Excision Repair Enzyme Specific for a Pyrimidine Dimer
Authors: Morikawa, K. / Matsumoto, O. / Tsujimoto, M. / Katayanagi, K. / Ariyoshi, M. / Doi, T. / Ikehara, M. / Inaoka, T. / Ohtsuka, E.
#5: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary Crystallographic Study of Pyrimidine Dimer-Specific Excision Repair Enzyme from Bacteriophage T4
Authors: Morikawa, K. / Tsujimoto, M. / Ikehara, M. / Inaoka, T. / Ohtsuka, E.
History
DepositionSep 8, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 31, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2013Group: Derived calculations / Other
Revision 1.4Nov 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')
C: DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')
A: PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))


Theoretical massNumber of molelcules
Total (without water)23,9173
Polymers23,9173
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.820, 118.820, 36.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: DNA chain DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')


Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')


Mass: 3985.613 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))


Mass: 15972.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: DENV / Gene (production host): DENV / Production host: Escherichia coli (E. coli) / Keywords: MUTANT E23Q / References: UniProt: P04418
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BIS-TRIS-PROPANE_HCL11
3NH4 SULFATE11
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.38 mMprotein1drop
20.53 mMDNA1dropduplex
3150 mMTris-HCl1drop
433 %satammonium sulfate1drop
554 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Jun 3, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 5662 / % possible obs: 72 % / Observed criterion σ(F): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 50 Å / % possible obs: 72 % / Observed criterion σ(F): 2 / Num. measured all: 24907

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
ELMSdata reduction
RefinementResolution: 2.75→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.24 --
Rwork0.152 --
obs0.152 5447 72 %
Displacement parametersBiso mean: 7.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 527 0 143 1799
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 7.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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