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- PDB-3bq1: Insertion ternary complex of Dbh DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 3bq1
TitleInsertion ternary complex of Dbh DNA polymerase
Components
  • DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3')
  • DNA (5'-D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DNA polymerase / Y-family / lesion bypass / single-base deletion / -1 frameshift / 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


DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / 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 / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. ...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 / 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'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPata, J.D. / Wilson, R.C.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.
Authors: Wilson, R.C. / Pata, J.D.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_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.pdbx_dist_value / _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_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
P: DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3')
T: DNA (5'-D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3')
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1455
Polymers47,6143
Non-polymers5312
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-34.8 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.96, 124.96, 70.21
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3')


Mass: 3095.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer
#2: DNA chain DNA (5'-D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3')


Mass: 4472.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase IV / / 2.7.7.7 / Pol IV / Dbh


Mass: 40045.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: dbh / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: Q4JB80, DNA-directed DNA polymerase

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Non-polymers , 3 types, 43 molecules

#4: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG-3350, calcium acetate, glycerol, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1calcium acetate11
2calcium acetate12
3glycerol11
4glycerol12
5HEPES11
6HEPES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 15669 / % possible obs: 99.6 % / Observed criterion σ(I): -0.5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1IM4 and 1K1Q

1im4

1k1q


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.879 / SU B: 30.757 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.225 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.267 711 4.9 %RANDOM
Rwork0.204 ---
all0.207 14437 --
obs0.207 14437 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 466 31 41 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223316
X-RAY DIFFRACTIONr_angle_refined_deg1.2422.1814572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.725343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0324.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94615542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9841517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022253
X-RAY DIFFRACTIONr_nbd_refined0.2070.21356
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.0190.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.25
X-RAY DIFFRACTIONr_mcbond_it0.3391.51766
X-RAY DIFFRACTIONr_mcangle_it0.59322786
X-RAY DIFFRACTIONr_scbond_it0.82331901
X-RAY DIFFRACTIONr_scangle_it1.4114.51786
LS refinement shellResolution: 2.7→2.786 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 6 -
Rwork0.317 257 -
all-263 -
obs--98.13 %
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)
13.7732-1.72252.88872.956-2.24238.4046-0.1278-0.17590.09440.59390.2680.0603-0.16060.0261-0.1402-0.13640.1040.0034-0.26090.0108-0.169936.473123.7167-16.255
26.28923.26360.50725.1271-0.11774.4685-0.1621-0.5781-0.60951.5075-0.14181.51650.6813-0.74970.30390.76970.19210.31540.30220.05610.593625.49678.02723.1778
33.84780.35780.31887.43743.73259.3826-0.39650.3756-0.4833-0.35640.2454-0.32530.79840.19790.15110.10660.02550.03880.01670.0347-0.045146.0571-2.7752-25.863
42.3760.32690.536410.4653-0.76352.6938-0.06880.73580.6858-0.31830.0521.8674-0.484-0.29520.01690.36420.1741-0.1298-0.07670.26850.510729.0816-2.6905-16.7683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 1681 - 168
2X-RAY DIFFRACTION2AC169 - 232169 - 232
3X-RAY DIFFRACTION3AC233 - 344233 - 344
4X-RAY DIFFRACTION4PA1 - 101 - 10
5X-RAY DIFFRACTION4TB2 - 152 - 15

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