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- PDB-2w9c: Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine mo... -

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Basic information

Entry
Database: PDB / ID: 2w9c
TitleTernary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP
Components
  • (DNA POLYMERASE ...) x 2
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'
  • 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
KeywordsTRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / N2-DIMETHYL-G / METAL-BINDING / MUTATOR PROTEIN / DNA DAMAGE / DNA REPAIR / DNA-BINDING / TRANSFERASE / DNA REPLICATION / NUCLEOTIDYLTRANSFERASE / DNA / DPO4 / ADDUCT / CYTOPLASM / MAGNESIUM / POLYMERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / 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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEoff, R.L. / Zhang, H. / Kosekov, I.D. / Rizzo, C.J. / Egli, M. / Guengerich, F.P.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes.
Authors: Zhang, H. / Eoff, R.L. / Kosekov, I.D. / Rizzo, C.J. / Egli, M. / Guengerich, F.P.
History
DepositionJan 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 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 / struct_site
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.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 / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE IV
B: DNA POLYMERASE IV
C: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'
D: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'
E: 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
F: 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,27414
Polymers101,1646
Non-polymers1,1108
Water1,964109
1
A: DNA POLYMERASE IV
C: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'
E: 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1517
Polymers50,5963
Non-polymers5554
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-62 kcal/mol
Surface area19490 Å2
MethodPISA
2
B: DNA POLYMERASE IV
D: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'
F: 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1237
Polymers50,5683
Non-polymers5554
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-55 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.707, 101.622, 96.753
Angle α, β, γ (deg.)90.00, 92.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA POLYMERASE ... , 2 types, 2 molecules AB

#1: Protein DNA POLYMERASE IV / POL IV / DPO4


Mass: 41114.766 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
#2: Protein DNA POLYMERASE IV / POL IV / DPO4


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, 4 molecules CDEF

#3: DNA chain 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3'


Mass: 4080.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 13 BASE PRIMER DNA 5'-GGG GGA AGG ATT (DOC)- 3'
#4: DNA chain 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' / TEMPLATE DNA


Mass: 5400.534 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 18 BASE TEMPLATE DNA 5'-TCA C(M2G)G AAT CCT TCC CCC-3'

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Non-polymers , 3 types, 117 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.4 Å3/Da / Density % sol: 52.83 % / Description: NONE
Crystal growpH: 7.4
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, 1 MM DTTP.

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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: Jul 1, 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: 2.87→28.33 Å / Num. obs: 20782 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3
Reflection shellResolution: 2.87→3.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.2 / % possible all: 79.7

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Processing

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

2asd


Resolution: 2.9→28.33 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 44076.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1055 4.9 %RANDOM
Rwork0.252 ---
obs0.252 -97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.62 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--10.01 Å20 Å2-0.21 Å2
2---19.45 Å20 Å2
3---29.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.43 Å
Luzzati d res low-30 Å
Luzzati sigma a0.42 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.9→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 1180 64 109 6843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.492.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.87→3.05 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 142 4.7 %
Rwork0.338 --
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3DTTP.PARAMDTTP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP

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