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- PDB-2w8k: Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct... -

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Basic information

Entry
Database: PDB / ID: 2w8k
TitleY-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in syn orientation
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3'
  • 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsTRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / DNA / DPO4 / ADDUCT / N2-ALKYL / CYTOPLASM / MAGNESIUM / TRANSFERASE / METAL-BINDING / MUTATOR PROTEIN / DNA REPLICATION / NUCLEOTIDYLTRANSFERASE / COMPLEX / POLYMERASE / DNA DAMAGE / DNA REPAIR / DNA-BINDING / 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEoff, R.L. / Zhang, H. / Egli, M. / Guengerich, F.P.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts.
Authors: Zhang, H. / Eoff, R.L. / Kozekov, I.D. / Rizzo, C.J. / Egli, M. / Guengerich, F.P.
History
DepositionJan 16, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionJan 27, 2009ID: 2V4S
Revision 1.0Jan 27, 2009Provider: 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_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_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*DOC)-3'
T: 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5497
Polymers50,9693
Non-polymers5804
Water1,44180
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-64 kcal/mol
MethodPISA
Unit cell
Length a, b, c (Å)95.040, 103.910, 52.320
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*CP*DOC)-3'


Mass: 4369.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 14 BASE PRIMER DNA 5'-GGG GGA AGG ATT CC-3'
#3: DNA chain 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5512.662 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 18 BASE TEMPLATE DNA 5'-TCA C(N2G)G AAT CCT TCC CCC-3'

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Non-polymers , 3 types, 84 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsENGINEERED HEXA-HISTIDINE TAG AND LAST 11 RESIDUES ARE DISORDERED

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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: 2.6 Å3/Da / Density % sol: 56.3 % / Description: NONE
Crystal growpH: 8
Details: DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO; 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 4% GLYCEROL, 1 MM DGTP.

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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: Jun 11, 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: 3.1→30 Å / Num. obs: 9733 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.6
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.2 / % possible all: 95.1

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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: 3.1→19.97 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 82552.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 521 5.3 %RANDOM
Rwork0.233 ---
obs0.233 9806 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.93 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 88.9 Å2
Baniso -1Baniso -2Baniso -3
1-17.16 Å20 Å20 Å2
2---19.92 Å20 Å2
3---2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.45 Å
Luzzati d res low-30 Å
Luzzati sigma a0.79 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 613 34 80 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_scangle_it2.572.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 35 4.5 %
Rwork0.38 738 -
obs--43.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3DGTP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5WATER_REP.PARAM

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