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- PDB-2oh2: Ternary Complex of Human DNA Polymerase -

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Basic information

Entry
Database: PDB / ID: 2oh2
TitleTernary Complex of Human DNA Polymerase
Components
  • 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'
  • 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
  • DNA polymerase kappaPOLK
KeywordsTransferase/DNA / DNA Polymerase / 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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLone, S. / Townson, S.A. / Uljon, S.N. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
CitationJournal: To be Published
Title: Ternary complex of the catalytic core of human DNA polymerase Kappa with DNA and dTT
Authors: Lone, S. / Townson, S.A. / Uljon, S.N. / Johnson, R.E. / Brahma, A. / Nair, D.T. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
S: 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'
Q: 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
P: 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'
T: 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
A: DNA polymerase kappa
B: DNA polymerase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,98210
Polymers134,9696
Non-polymers1,0134
Water37821
1
S: 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'
Q: 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
A: DNA polymerase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9915
Polymers67,4843
Non-polymers5062
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'
T: 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
B: DNA polymerase kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9915
Polymers67,4843
Non-polymers5062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.150, 152.472, 217.389
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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DNA chain , 2 types, 4 molecules SPQT

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


Mass: 4066.648 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5379.466 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

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


Mass: 58038.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLK, DINB1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5464 / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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Non-polymers , 3 types, 25 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.54 Å3/Da / Density % sol: 65.28 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 21, 2005 / Details: mirrors
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 37532 / Num. obs: 37424 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.05→3.16 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 3531 random
Rwork0.231 --
all-37111 -
obs-35239 -
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-3.05 Å
Luzzati sigma a0.61 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 1006 60 21 7583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_bond_d0.077
X-RAY DIFFRACTIONc_dihedral_angle_d21.48
X-RAY DIFFRACTIONc_improper_angle_d1.037

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