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- PDB-2wtf: DNA polymerase eta in complex with the cis-diammineplatinum (II) ... -

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Basic information

Entry
Database: PDB / ID: 2wtf
TitleDNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3- GTG intrastrand cross-link
Components
  • 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'
  • 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'
  • DNA POLYMERASE ETA
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / NUCLEOTIDYLTRANSFERASE / TRANSLESION DNA SYNTHESIS / TRANSFERASE / DNA-BINDING / DNA SYNTHESIS / DNA REPLICATION / MUTATOR PROTEIN / DNA DAMAGE / DNA REPAIR
Function / homology
Function and homology information


Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA-directed DNA polymerase ...Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / mitochondrion / zinc ion binding / nucleus
Similarity search - Function
DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / 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 ...DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / 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 / 5' to 3' exonuclease, C-terminal subdomain / 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
Cisplatin / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReissner, T. / Schneider, S. / Ziv, O. / Schorr, S. / Livneh, Z. / Carell, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Crystal Structure of a Cisplatin-(1,3-Gtg) Cross-Link within DNA Polymerase Eta.
Authors: Reissner, T. / Schneider, S. / Schorr, S. / Carell, T.
History
DepositionSep 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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_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.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
A: DNA POLYMERASE ETA
B: DNA POLYMERASE ETA
O: 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'
P: 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'
S: 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'
T: 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,20320
Polymers137,2206
Non-polymers1,98314
Water2,162120
1
A: DNA POLYMERASE ETA
O: 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'
P: 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5619
Polymers68,6103
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-75.1 kcal/mol
Surface area26160 Å2
MethodPISA
2
B: DNA POLYMERASE ETA
S: 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'
T: 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,64111
Polymers68,6103
Non-polymers1,0328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-97.8 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.240, 103.240, 292.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8092, -0.2888, 0.5116), (-0.3173, -0.518, -0.7943), (0.4944, -0.8052, 0.3275)
Vector: -2.268, 1.101, 1.719)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA POLYMERASE ETA / DNA POLYMERASE ETA RAD30 / RADIATION-SENSITIVE PROTEIN 30


Mass: 60708.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PDEST007 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q04049, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules OSPT

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


Mass: 5089.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CISPLATIN 1,3 GTG INTRASTRAND CROSS-LINK BETWEEN O 3 AND O 5, S 3 AND S 5
#3: DNA chain 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'


Mass: 2811.846 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 134 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-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.: 10 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.04 Å3/Da / Density % sol: 48 %
Description: MR PHASES WERE COMBINED WITH PLATINUM SAD PHASES USING SHARP
Crystal growDetails: 4MG/ML, 11-14% PEG3350, 0.15-0.2M CACL2, 0.1M ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0766
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0766 Å / Relative weight: 1
ReflectionResolution: 2.5→48.68 Å / Num. obs: 55019 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
SHARPphasing
REFMAC5.5.0070refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JIH

1jih


Resolution: 2.5→48 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.913 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A 510-513 DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26871 2793 5.1 %RANDOM
Rwork0.22712 ---
obs0.22922 52206 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8013 878 76 120 9087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229239
X-RAY DIFFRACTIONr_bond_other_d0.0060.026096
X-RAY DIFFRACTIONr_angle_refined_deg1.6332.112659
X-RAY DIFFRACTIONr_angle_other_deg0.946314945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68951017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54324.688352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.131151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7481540
X-RAY DIFFRACTIONr_chiral_restr0.0860.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8341.55057
X-RAY DIFFRACTIONr_mcbond_other0.1481.52055
X-RAY DIFFRACTIONr_mcangle_it1.628174
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32634182
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6944.54484
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 196 -
Rwork0.382 3849 -
obs--99.51 %

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