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- PDB-2r8i: Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N... -

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Basic information

Entry
Database: PDB / ID: 2r8i
TitleSelectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2-Propanodeoxyguanosine (PdG) by the Sulfolobus solfataricus DNA Polymerase Dpo4 Polymerase
Components
  • DNA (5'-D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DC)-3')
  • DNA (5'-D(*DTP*DCP*DAP*DTP*(P)P*DGP*DAP*DAP*DTP*DCP*DCP*DTP*DTP*DCP*DCP*DCP*DCP*DC)-3')
  • DNA polymerase IV
KeywordsREPLICATION / TRANSFERASE/DNA / exocyclic adducts / replication bypass / translesion / polymerase / frameshifting / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsWang, Y. / Saleh, S. / Marnette, L.J. / Egli, M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2008
Title: Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV
Authors: Wang, Y. / Musser, S.K. / Saleh, S. / Marnett, L.J. / Egli, M. / Stone, M.P.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: DNA (5'-D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DC)-3')
T: DNA (5'-D(*DTP*DCP*DAP*DTP*(P)P*DGP*DAP*DAP*DTP*DCP*DCP*DTP*DTP*DCP*DCP*DCP*DCP*DC)-3')
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3947
Polymers49,7823
Non-polymers6114
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-65 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.2, 101.9, 52.7
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DC)-3')


Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: PDB-2R8G
#2: DNA chain DNA (5'-D(*DTP*DCP*DAP*DTP*(P)P*DGP*DAP*DAP*DTP*DCP*DCP*DTP*DTP*DCP*DCP*DCP*DCP*DC)-3')


Mass: 5427.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: PDB-2R8G

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase IV / / E.C.2.7.7.7 / dpo4 / Pol IV


Mass: 40257.879 Da / Num. of mol.: 1 / Mutation: R332A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea)
Description: purified using heat denaturation, Ni2+-nitriloacetate chromatography, and ion-exchange chromatography
Gene: dbh, dpo4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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Non-polymers , 3 types, 108 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.92 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 35739 / Num. obs: 25742

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→50 Å
RfactorNum. reflection
Rfree0.266 25742
Rwork0.22 -
obs0.2201 25742
all-35739
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 616 33 105 3497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d21.61
X-RAY DIFFRACTIONc_improper_angle_d1.11

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