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- PDB-2w7p: Structure and Activity of Bypass Synthesis by Human DNA Polymeras... -

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Basic information

Entry
Database: PDB / ID: 2w7p
TitleStructure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
  • 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE KAPPAPOLK
KeywordsDNA BINDING PROTEIN / 8-OXO-2P-DEOXY-GUANOSINE-5P-MONOPHOSPHATE / TRANSLESION DNA POLYMERASE / HUMAN DNA POLYMERASE KAPPA / DATP / DNA REPAIR / DNA DAMAGE / DNA-BINDING PROTEIN
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV ...nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I ...DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsIrimia, A. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine Adduct.
Authors: Irimia, A. / Eoff, R.L. / Guengerich, F.P. / Egli, M.
History
DepositionDec 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.conn_type_id / _struct_conn.id / _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_conn_type.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
A: DNA POLYMERASE KAPPA
B: DNA POLYMERASE KAPPA
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
F: 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
T: 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,19012
Polymers135,0476
Non-polymers1,1436
Water21612
1
A: DNA POLYMERASE KAPPA
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
T: 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0956
Polymers67,5233
Non-polymers5713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-63 kcal/mol
Surface area26750 Å2
MethodPISA
2
B: DNA POLYMERASE KAPPA
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
F: 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0956
Polymers67,5233
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-59 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.829, 220.847, 119.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA POLYMERASE KAPPA / POLK / DINB / DINP


Mass: 58038.293 Da / Num. of mol.: 2 / Fragment: RESIDUES 19-526
Source method: isolated from a genetically manipulated source
Details: HUMAN DNA POLYMERASE KAPPA CATALYTIC CORE, RESIDUES 19-526
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: POLK, DINB1 / Plasmid: PBG101 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules EPFT

#2: DNA chain 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'


Mass: 4096.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PRIMER
#3: DNA chain 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3'


Mass: 5388.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TEMPLATE

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Non-polymers , 3 types, 18 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.4 Å3/Da / Density % sol: 75.7 % / Description: NONE
Crystal growpH: 7
Details: 70 MM NACL,1.35 MM KCL, 2.1 MM NA2HPO4, 0.75 MM KH2PO4, PH 7.4, 5 MM GLYCEROL, 0.5 MM EDTA, 0.5 MM DTT, 2.5 MM 2-MERCHAPTOETHANOL, 0.05% NONIDET P-40, 2.5 MM CACL2, 2.5 MM DATP, 11% ...Details: 70 MM NACL,1.35 MM KCL, 2.1 MM NA2HPO4, 0.75 MM KH2PO4, PH 7.4, 5 MM GLYCEROL, 0.5 MM EDTA, 0.5 MM DTT, 2.5 MM 2-MERCHAPTOETHANOL, 0.05% NONIDET P-40, 2.5 MM CACL2, 2.5 MM DATP, 11% PEG5000MME, 0.1 M AMMONIUM ACETATE,10 MM MES PH 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2007
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.71→44.65 Å / Num. obs: 23041 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4
Reflection shellResolution: 3.7→3.93 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / % possible all: 86.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W7O

2w7o


Resolution: 3.71→44.65 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 5450614.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1113 4.8 %RANDOM
Rwork0.236 ---
obs0.236 23026 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.45 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 95.5 Å2
Baniso -1Baniso -2Baniso -3
1-25.2 Å20 Å20 Å2
2---47.35 Å20 Å2
3---22.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å1 Å
Refinement stepCycle: LAST / Resolution: 3.71→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 1136 64 12 8125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 3.7→3.93 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 158 4.6 %
Rwork0.351 3261 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA1.PARAMDNA-RNA1.TOP
X-RAY DIFFRACTION3DATP.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMDATP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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