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- PDB-3gim: Dpo4 extension ternary complex with oxoG(anti)-G(syn) pair -

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Basic information

Entry
Database: PDB / ID: 3gim
TitleDpo4 extension ternary complex with oxoG(anti)-G(syn) pair
Components
  • 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DNA POLYMERASE / 8-OXOGUANINE / Y-FAMILY / LESION BYPASS / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Transferase / 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 P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRechkoblit, O. / Malinina, L. / Patel, D.J.
CitationJournal: Structure / Year: 2009
Title: Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
Authors: Rechkoblit, O. / Malinina, L. / Cheng, Y. / Geacintov, N.E. / Broyde, S. / Patel, D.J.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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_ref_seq / struct_ref_seq_dif / 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_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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _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
D: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-3'
E: 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0657
Polymers48,4383
Non-polymers6274
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-34.5 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.668, 111.924, 53.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 38945.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / DSM 1617 / JCM 11322 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL(STRATAGENE) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules DE

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


Mass: 4086.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer strand
#3: DNA chain 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'


Mass: 5405.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA OXOG-modified template strand

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Non-polymers , 3 types, 45 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.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 100 mM Calcium acetate, 10% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2Calcium acetate12
3PEG 400013

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2005
Details: 6144 x 6144 pixel elements with an effective pixel size less than 60x60 micron and resolution of order 90x90 micron
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 15930 / % possible obs: 93.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Χ2: 1.076 / Net I/σ(I): 18.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.7-2.85.10.493311981.04572.7
2.8-2.915.60.48113601.10782.2
2.91-3.046.10.4215021.08489.9
3.04-3.26.30.27216061.06496.3
3.2-3.46.50.19616681.07399.3
3.4-3.666.50.12816831.04699.5
3.66-4.036.40.09616861.068100
4.03-4.66.30.06717031.05999.6
4.6-5.776.20.05817200.98299.1
5.77-2060.05618041.2398.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GIK

3gik


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0 / SU B: 31.854 / SU ML: 0.319 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.99 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 797 5 %RANDOM
Rwork0.214 ---
obs0.217 15879 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.1 Å2 / Biso mean: 56.274 Å2 / Biso min: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1-8.92 Å20 Å20 Å2
2---5.51 Å20 Å2
3----3.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 630 34 41 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223540
X-RAY DIFFRACTIONr_angle_refined_deg1.5222.2264885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24723.607122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4411524
X-RAY DIFFRACTIONr_chiral_restr0.1140.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022361
X-RAY DIFFRACTIONr_nbd_refined0.2650.31558
X-RAY DIFFRACTIONr_nbtor_refined0.3380.52354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.5228
X-RAY DIFFRACTIONr_metal_ion_refined0.3470.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.54
X-RAY DIFFRACTIONr_mcbond_it0.4311.51743
X-RAY DIFFRACTIONr_mcangle_it0.69822766
X-RAY DIFFRACTIONr_scbond_it0.91732228
X-RAY DIFFRACTIONr_scangle_it1.6324.52119
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 51 -
Rwork0.336 805 -
all-856 -
obs--72.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2068-0.57720.11917.9912-4.35055.2602-0.1452-0.11590.05670.46660.49980.5391-0.325-0.4889-0.3546-0.25990.002-0.0113-0.08960.0437-0.180621.76518.67312.232
22.7370.64371.06314.1908-1.42232.43170.1534-0.70510.35941.04390.62931.3370.0628-1.1194-0.78270.11210.06560.25350.39450.21580.218211.66610.59721.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2D802 - 814
3X-RAY DIFFRACTION2E901 - 918
4X-RAY DIFFRACTION2A414

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