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- PDB-2v4r: Non-productive complex of the Y-family DNA polymerase Dpo4 with d... -

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Basic information

Entry
Database: PDB / ID: 2v4r
TitleNon-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'
  • 5'-D(*TP*CP*AP*CP*M1GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA-BINDING / METAL-BINDING / DNA REPLICATION / MUTATOR PROTEIN / NUCLEOTIDYLTRANSFERASE / DNA ADDUCT / DNA DAMAGE / DNA REPAIR / DPO4 / M1DG / CYTOPLASM / MAGNESIUM
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 / 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'-DEOXYGUANOSINE-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: 2.5 Å
AuthorsEoff, R.L. / Stafford, J.B. / Szekely, J. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. / Marnett, L.J.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct.
Authors: Eoff, R.L. / Stafford, J.B. / Szekely, J. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. / Marnett, L.J.
History
DepositionSep 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_entity_src_syn / reflns / reflns_shell / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 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_conn_type / 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.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 / _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
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*CP*M1GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2197
Polymers50,5923
Non-polymers6274
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-60 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.545, 102.537, 52.176
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


Mass: 41086.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / 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 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 / Details: 13 BASE PRIMER DNA 5'-GGG GGA AGG ATT C-3' / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*TP*CP*AP*CP*M1GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5408.513 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 18 BASE TEMPLATE DNA 5'-TCA C(M1G)G AAT CCT TCC CCC-3'
Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 138 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#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


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN TERMINAL HEXA-HISTIDINE TAG AND MISSING LAST 11 RESIDUES

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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: 3.1 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.4
Details: 7.5% POLYETHYLENE GLYCOL 3350, 100 MM CALCIUM ACETATE, 25 MM TRIS HCL (PH 7.4), 100 MM SODIUM CHLORIDE, 2.5% GLYCEROL, 1 MM DGTP, 5 MM CALCIUM CHLORIDE.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17552 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.89
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQR

2bqr


Resolution: 2.5→29.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 72280.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 848 4.8 %RANDOM
Rwork0.218 ---
obs0.218 17552 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9285 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.72 Å20 Å20 Å2
2---6.54 Å20 Å2
3----3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-30 Å
Luzzati sigma a0.52 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 611 34 134 3533
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.48
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.142.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.6 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 87 4.3 %
Rwork0.324 1923 -
obs--64.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: WATER.TOP

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