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- PDB-3gii: Dpo4 extension ternary complex with disordered A opposite an oxoG... -

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Basic information

Entry
Database: PDB / ID: 3gii
TitleDpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation
Components
  • 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
  • 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-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, 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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Sep 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_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.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_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_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*(2DA))-3'
E: 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3618
Polymers48,7113
Non-polymers6505
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-28.8 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.761, 111.646, 52.708
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*(2DA))-3'


Mass: 4070.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer
#3: DNA chain 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'


Mass: 5694.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: OXOG-modified template strand

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Non-polymers , 4 types, 71 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
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: 24-ID-C / Wavelength: 0.97942 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: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 17030 / Num. obs: 16924 / % possible obs: 94.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.2
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.6 / Num. unique all: 975 / % possible all: 71.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ASD

2asd


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.176 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.687 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 856 5.1 %RANDOM
Rwork0.202 ---
obs0.205 16924 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.56 Å2 / Biso mean: 49.029 Å2 / Biso min: 26.48 Å2
Baniso -1Baniso -2Baniso -3
1-5.08 Å20 Å20 Å2
2---1.85 Å20 Å2
3----3.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 628 35 66 3469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223525
X-RAY DIFFRACTIONr_bond_other_d0.0010.022294
X-RAY DIFFRACTIONr_angle_refined_deg1.6512.2274866
X-RAY DIFFRACTIONr_angle_other_deg0.92335623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2485340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71523.636121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96915560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4221524
X-RAY DIFFRACTIONr_chiral_restr0.110.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
X-RAY DIFFRACTIONr_nbd_refined0.2130.2687
X-RAY DIFFRACTIONr_nbd_other0.1950.22381
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21629
X-RAY DIFFRACTIONr_nbtor_other0.0820.21726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2610.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.24
X-RAY DIFFRACTIONr_mcbond_it0.4721.51707
X-RAY DIFFRACTIONr_mcbond_other0.0631.5688
X-RAY DIFFRACTIONr_mcangle_it0.84322759
X-RAY DIFFRACTIONr_scbond_it1.15231968
X-RAY DIFFRACTIONr_scangle_it1.8374.52107
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 41 -
Rwork0.334 880 -
all-921 -
obs--71.56 %
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)
10.6746-0.1814-0.01552.3402-0.57311.9552-0.0266-0.06810.0519-0.02840.06750.1591-0.1566-0.3078-0.0409-0.1140.0174-0.0474-0.0849-0.003-0.115721.441717.402712.4807
22.4648-0.80440.47673.5787-0.53191.42840.1084-0.45570.22680.47970.14970.65-0.0927-0.6972-0.2581-0.0433-0.05240.04750.15320.0480.045310.01459.484422.9242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2D802 - 813
3X-RAY DIFFRACTION2E901 - 919

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