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- PDB-2bqr: DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4.... -

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Basic information

Entry
Database: PDB / ID: 2bqr
TitleDNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'
  • 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsTRANSFERASE / P2 DNA POLYMERASE IV / 1N2-ETHENOGUANINE ADDUCT / TRANSLESION DNA POLYMERASE / DATP / NUCLEOTIDYLTRANSFERASE
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: 2.37 Å
AuthorsIrimia, A. / Loukachevitch, L.V. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine.
Authors: Zang, H. / Goodenough, A.K. / Choi, J.Y. / Irimia, A. / Loukachevitch, L.V. / Kozekov, I.D. / Angel, K.C. / Rizzo, C.J. / Egli, M. / Guengerich, F.P.
History
DepositionApr 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_conn_type
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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE IV
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'
T: 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2067
Polymers50,5953
Non-polymers6114
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.528, 103.027, 53.097
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: 41086.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Gene: DPO4 / Plasmid: PET22B/DPO4-NHIS / 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 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
#3: DNA chain 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5411.514 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 18-MER DNA TEMPLATE CONTAINING 1, N2-ETHENOGUANINE ADDUCT

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Non-polymers , 3 types, 113 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE FIRST NUCLEOTIDE OF THE TEMPLATE DNA IS NOT OBSERVED IN THE STRUCTURE.

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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: 2.61 Å3/Da / Density % sol: 52.26 %
Description: THE STARTING MODEL WAS THE PDB FILE WITH THE ACCESSION CODE 2BQ3. ITS POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT.
Crystal growpH: 7
Details: 16% PEG 3350, 0.1 M HEPES PH 7.0, 100 MM CALCIUM ACETATE, 2.5% GLYCEROL, 0.5 MM DATP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.991
DetectorType: MARRESEARCH MAR300 / Detector: IMAGE PLATE / Date: Nov 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991 Å / Relative weight: 1
ReflectionResolution: 2.37→42.32 Å / Num. obs: 20350 / % possible obs: 92.6 % / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 2.37→2.52 Å / % possible all: 65.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQ3

2bq3


Resolution: 2.37→42.32 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1324284.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FIRST NUCLEOTIDE OF THE TEMPLATE DNA IS NOT OBSERVED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 998 4.9 %RANDOM
Rwork0.223 ---
obs0.223 20350 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1304 Å2 / ksol: 0.311469 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.2 Å20 Å20 Å2
2---5.38 Å20 Å2
3---1.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-42.32 Å
Luzzati sigma a0.44 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.37→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 611 33 109 3497
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 119 5 %
Rwork0.407 2254 -
obs--65.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ATP.PARAMATP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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