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- PDB-2end: CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ... -

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Basic information

Entry
Database: PDB / ID: 2end
TitleCRYSTAL 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
ComponentsENDONUCLEASE V
KeywordsENDONUCLEASE
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.45 Å
AuthorsVassylyev, D.G. / Ariyoshi, M. / Matsumoto, O. / Katayanagi, K. / Ohtsuka, E. / Morikawa, K.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.
Authors: Morikawa, K. / Ariyoshi, M. / Vassylyev, D.G. / Matsumoto, O. / Katayanagi, K. / Ohtsuka, E.
#1: 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, T. / Katayanagi, K. / Ariyoshi, M. / Doi, T. / Ikehara, M. / Inaoka, T. / Ohtsuka, E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Role of the Basic Amino Acid Cluster and Glu-23 in Pyrimidine Dimeer 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.
#3: 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
DepositionAug 8, 1994Processing site: BNL
SupersessionOct 15, 1994ID: 1END
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDONUCLEASE V


Theoretical massNumber of molelcules
Total (without water)16,1051
Polymers16,1051
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.310, 40.110, 37.590
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDONUCLEASE V


Mass: 16104.574 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 / References: UniProt: P04418, EC: 3.1.25.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.5 / Method: vapor diffusion / Details: Morikawa, K., (1988) J. Mol. Biol., 202, 683.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mM1dropKCl
38 mMsodium cacodylate/HCl1drop
45 %(w/v)PEG40001drop
515 %PEG1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.45 Å / % possible obs: 80.2 % / Rmerge(I) obs: 0.048

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.45→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.161 17350
Refinement stepCycle: LAST / Resolution: 1.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 0 172 1301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0741.5
X-RAY DIFFRACTIONp_mcangle_it1.6282
X-RAY DIFFRACTIONp_scbond_it2.2422
X-RAY DIFFRACTIONp_scangle_it3.5432.5
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.10.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.20.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1810.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor11.815
X-RAY DIFFRACTIONp_orthonormal_tor26.920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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