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- PDB-4u7c: Structure of DNA polymerase kappa in complex with benzopyrene add... -

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Basic information

Entry
Database: PDB / ID: 4u7c
TitleStructure of DNA polymerase kappa in complex with benzopyrene adducted DNA
Components
  • DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3')
  • DNA polymerase kappaPOLK
KeywordsTRANSFERASE/DNA / benzo[a]pyrene-N2-Guanine / DNA replication / DNA damage tolerance / polymerase kappa / Environment pollution / TRANSFERASE-DNA complex
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
Chem-0KX / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJha, V.K. / Ling, H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-67128 Canada
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa.
Authors: Jha, V. / Bian, C. / Xing, G. / Ling, H.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Derived calculations
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jun 15, 2016Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
C: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3')
D: DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')
P: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3')
T: DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,74114
Polymers126,3806
Non-polymers1,3618
Water2,036113
1
A: DNA polymerase kappa
C: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3')
D: DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7876
Polymers63,1903
Non-polymers5973
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-33 kcal/mol
Surface area24440 Å2
MethodPISA
2
B: DNA polymerase kappa
P: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3')
T: DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9558
Polymers63,1903
Non-polymers7655
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-34 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 130.170, 166.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase kappa / POLK / DINB protein / DINP


Mass: 56139.246 Da / Num. of mol.: 2 / Fragment: UNP residues 27-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLK, DINB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CPDT

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


Mass: 2780.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')


Mass: 4269.909 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 5 types, 121 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: PEG 400, ammonium iodide

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→47.111 Å / Num. obs: 34235 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OH2

2oh2


Resolution: 2.8→47.111 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 877 2.57 %
Rwork0.2123 --
obs0.2133 34189 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 946 83 113 7862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068005
X-RAY DIFFRACTIONf_angle_d1.05710995
X-RAY DIFFRACTIONf_dihedral_angle_d20.5983095
X-RAY DIFFRACTIONf_chiral_restr0.0441255
X-RAY DIFFRACTIONf_plane_restr0.0041234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.97540.38681610.35655466X-RAY DIFFRACTION98
2.9754-3.20510.32981490.29185494X-RAY DIFFRACTION99
3.2051-3.52750.30771280.23625519X-RAY DIFFRACTION98
3.5275-4.03780.28751530.20945562X-RAY DIFFRACTION99
4.0378-5.08620.24111470.1855586X-RAY DIFFRACTION99
5.0862-47.11760.18661390.18445685X-RAY DIFFRACTION96

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