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- PDB-2fcc: Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Cov... -

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Basic information

Entry
Database: PDB / ID: 2fcc
TitleCrystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site
Components
  • DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3')
  • Endonuclease V
KeywordsHYDROLASE / T4-Pdg / Pyrimidine Dimer / DNA repair / endonuclease / enzyme-DNA complex / covalent intermediate
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGolan, G. / Zharkov, D.O. / Fernandes, A.S. / Dodson, M.L. / McCullough, A.K. / Grollman, A.P. / Lloyd, R.S. / Shoham, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine Covalent Complex with Abasic Site-containing DNA.
Authors: Golan, G. / Zharkov, D.O. / Grollman, A.P. / Dodson, M.L. / McCullough, A.K. / Lloyd, R.S. / Shoham, G.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
C: DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
D: DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3')
E: DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3')
A: Endonuclease V
B: Endonuclease V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,48610
Polymers48,1106
Non-polymers3764
Water3,297183
1
C: DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
D: DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3')
A: Endonuclease V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3396
Polymers24,0553
Non-polymers2843
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3')
B: Endonuclease V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1474
Polymers24,0553
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.059, 184.059, 100.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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DNA chain , 2 types, 4 molecules CEDF

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


Mass: 3863.531 Da / Num. of mol.: 2 / Fragment: ds oligonucleotide containing AP site / Source method: obtained synthetically / Details: Chemically synthesized.
#2: DNA chain DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3')


Mass: 4218.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized.

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Protein , 1 types, 2 molecules AB

#3: Protein Endonuclease V


Mass: 15973.376 Da / Num. of mol.: 2 / Fragment: T4-PDG
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 / Production host: Escherichia coli (E. coli) / Strain (production host): AB2480 / References: UniProt: P04418, EC: 3.1.25.1

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Non-polymers , 3 types, 187 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2 M (NH4)2SO4 and 0.1 M sodium citrate buffer (pH 6.4), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9188 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 81403 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.393 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAS

1vas


Resolution: 2.3→39.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 464806.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 4032 5 %RANDOM
Rwork0.249 ---
obs0.249 81403 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1503 Å2 / ksol: 0.332785 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20.6 Å20 Å2
2--2.36 Å20 Å2
3----4.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 1036 22 183 3495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 602 4.8 %
Rwork0.289 11988 -
obs--89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna-ped.paramdna-rna-ped.top
X-RAY DIFFRACTION3gol.pargol.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5ion.paramion.top

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