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- PDB-2j6s: Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O... -

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Basic information

Entry
Database: PDB / ID: 2j6s
TitleTernary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3'
  • 5'-D(*TP*CP*AP*TP*XP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / MUTATOR PROTEIN / DNA REPLICATION / O6-METHYLGUANINE / TRANSFERASE / METAL-BINDING / DNA POLYMERASE / TRANSLESION DNA SYNTHESIS / DNA-DIRECTED DNA POLYMERASE / DPO4 / MAGNESIUM / DNA REPAIR / DNA DAMAGE / DNA-BINDING / NUCLEOTIDYLTRANSFERASE / SULFOLOBUS SOLFATARICUS
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIrimia, A. / Eoff, R.L. / Guengerich, F.P. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred.
Authors: Eoff, R.L. / Irimia, A. / Egli, M. / Guengerich, F.P.
History
DepositionOct 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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*CP*C)-3'
T: 5'-D(*TP*CP*AP*TP*XP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4867
Polymers50,8743
Non-polymers6114
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.682, 103.271, 52.674
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: STRAIN: P2 / Description: 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*CP*C)-3' / 14-MER PRIMER


Mass: 4385.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'GGGGGAAGGATTCC3'
#3: DNA chain 5'-D(*TP*CP*AP*TP*XP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3' / 18MER TEMPLATE


Mass: 5401.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'TCAT G32 GAATCCTTCCCCC3'

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Non-polymers , 3 types, 128 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.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL 6 HISTIDINE-TAG ADDED COMPARED TO UNIPROT Q97W02 SEQUENCE.

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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: 2.53 Å3/Da / Density % sol: 51.54 %
Crystal growpH: 7.4
Details: 7.5% PEG 3350, 25 MM TRIS_HCL PH 7.4, 100 MM CA(CH3CO2)2, 50MM NACL, 2.5% GLYCEROL, 5MM CACL2, AND 1MM DATP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Mar 22, 2006 / Details: BRUKER MONTEL CONFOCAL MULTILAYER MIRRORS
RadiationMonochromator: BRUKER MONTEL CONFOCAL MULTILAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→18.1 Å / Num. obs: 18215 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.69 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.36
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.51 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C22

2c22


Resolution: 2.5→18.09 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1255272.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 884 4.9 %RANDOM
Rwork0.234 ---
obs0.234 18215 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.3628 Å2 / ksol: 0.316845 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å20 Å20 Å2
2--0.01 Å20 Å2
3----4.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-50 Å
Luzzati sigma a0.46 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 609 33 124 3510
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 142 4.8 %
Rwork0.358 2834 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP1.PARAMDNA-RNA1.TOP
X-RAY DIFFRACTION3ATP.PARAMATP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER_REP.TOP

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