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- PDB-5edw: Ternary structure of Dpo4 bound to G in the template base paired ... -

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Basic information

Entry
Database: PDB / ID: 5edw
TitleTernary structure of Dpo4 bound to G in the template base paired with incoming dTTP
Components
  • DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
  • DNA polymerase IV
Keywordstransferase/dna / DNA polymerase / 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 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 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Sulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKoag, M.-C. / Lee, S.
CitationJournal: To Be Published
Title: Structure of Dpo4 DNA polymerase replicating across the genotoxic N7-methylguanine lesion
Authors: Koag, M.-C. / Lee, S.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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 IV
T: DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4207
Polymers48,8183
Non-polymers6024
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-77 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.516, 101.994, 52.864
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 A

#1: Protein DNA polymerase IV / Pol IV


Mass: 39019.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

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


Mass: 5701.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus P2 (archaea)
#3: DNA chain DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')


Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus P2 (archaea)

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Non-polymers , 3 types, 49 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 12 to 18% PEG 3350, 100 mM HEPES, 100 mM calcicum acetate, and 2.5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.62→20 Å / Num. obs: 16600 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 23.25
Reflection shellResolution: 2.62→2.67 Å / Mean I/σ(I) obs: 1.82

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S0N

1s0n


Resolution: 2.62→19.975 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 0.22 / Phase error: 29.59
RfactorNum. reflection% reflection
Rfree0.2842 801 5.09 %
Rwork0.2195 --
obs0.2228 15751 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.62→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 650 0 45 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053540
X-RAY DIFFRACTIONf_angle_d0.7554903
X-RAY DIFFRACTIONf_dihedral_angle_d22.7822069
X-RAY DIFFRACTIONf_chiral_restr0.045557
X-RAY DIFFRACTIONf_plane_restr0.003505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6201-2.78380.36121350.29542206X-RAY DIFFRACTION86
2.7838-2.99810.37191240.28192351X-RAY DIFFRACTION91
2.9981-3.29860.35091250.2512480X-RAY DIFFRACTION96
3.2986-3.77310.28961490.22552567X-RAY DIFFRACTION99
3.7731-4.74320.27161240.19612616X-RAY DIFFRACTION99
4.7432-19.97570.23061440.19432730X-RAY DIFFRACTION99

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