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- PDB-3m9m: Crystal Structure of Dpo4 in complex with DNA containing the majo... -

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Basic information

Entry
Database: PDB / ID: 3m9m
TitleCrystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion
Components
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTransferase/DNA / Dpo4 / translesion DNA synthesis / TLS / cisplatin / Y-family DNA polymerase / protein-DNA complex / DNA / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Transferase / Transferase-DNA complex
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
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 / 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 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 / 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 / CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWong, J.H.Y. / Ling, H.
CitationJournal: Embo J. / Year: 2010
Title: Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4.
Authors: Wong, J.H. / Brown, J.A. / Suo, Z. / Blum, P. / Nohmi, T. / Ling, H.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.entity_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.entity_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,97812
Polymers49,7583
Non-polymers1,2209
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-89 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.576, 101.193, 52.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules B

#1: Protein DNA polymerase IV / / Pol IV


Mass: 40257.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

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


Mass: 4154.722 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5345.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 5 types, 60 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 0.2M calcium acetate, 5% glycerol, 15% PEG 3350, 200mM NaCl, pH 7.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0781 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Mar 12, 2008
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 12180 / Num. obs: 12009 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Χ2: 1.161 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-33.40.6711661.08199.4
3-3.123.40.43411821.24999.2
3.12-3.273.50.22912141.09299.2
3.27-3.443.50.14611571.06699.6
3.44-3.653.50.10511921.07498.8
3.65-3.943.50.07311931.08999
3.94-4.333.50.04911941.1399.2
4.33-4.963.50.04712161.43198.9
4.96-6.243.40.04412321.35298.6
6.24-503.30.02312631.03595

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JX4

1jx4


Resolution: 2.9→45 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.748 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 818 6.7 %Random
Rwork0.285 ---
all0.286 12007 --
obs0.286 11987 98.5 %-
Solvent computationBsol: 32.47 Å2
Displacement parametersBiso max: 137.45 Å2 / Biso mean: 63.213 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1--11.092 Å20 Å20 Å2
2--3.739 Å20 Å2
3---7.353 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 554 53 51 3401
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg1.512
X-RAY DIFFRACTIONc_mcbond_it3.4521.5
X-RAY DIFFRACTIONc_scbond_it3.9182
X-RAY DIFFRACTIONc_mcangle_it5.6412
X-RAY DIFFRACTIONc_scangle_it6.4512.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_jw_020210_gg1.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ctp_par_121707.txt
X-RAY DIFFRACTION6gol_xplor_par.txt

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