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- PDB-3bq0: Pre-insertion binary complex of Dbh DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 3bq0
TitlePre-insertion binary 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 ...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
DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Revision 1.3Aug 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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6544
Polymers47,6143
Non-polymers401
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-26.3 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.416, 119.416, 68.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-411-

HOH

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Components

#1: 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
#2: 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 / Source: (synth.) synthetic construct (others)
#3: 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 / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
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: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 14027 / % possible obs: 89.3 % / Observed criterion σ(I): -1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 35.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.4 / % possible all: 81.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1im4

1k1q


Resolution: 2.6→19.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU B: 33.501 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 9.365 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27904 679 4.9 %RANDOM
Rwork0.21387 ---
obs0.21711 13125 88.15 %-
all-13804 --
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: 52.826 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20 Å2
2--3.07 Å20 Å2
3----6.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 462 1 110 3277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2462.1724489
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5624.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77715542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7581517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022221
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21543
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22150
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3981.51749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69822760
X-RAY DIFFRACTIONr_scbond_it0.85931849
X-RAY DIFFRACTIONr_scangle_it1.4664.51729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 41 -
Rwork0.324 847 -
obs--79.5 %
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)
12.6406-0.79852.98851.6048-0.95876.7841-0.08510.16650.07920.09410.1154-0.1651-0.1961-0.0867-0.0303-0.27610.2083-0.0064-0.1548-0.0236-0.17732.360221.7902-14.5178
23.29420.735-1.36223.1867-0.85912.5527-0.56420.4422-1.21180.56150.28340.58951.1664-0.63480.28080.42180.10850.12580.2582-0.10290.372325.67395.67015.4727
37.25915.00316.504714.683717.98630.3723-0.02570.5177-0.68660.39111.0223-1.09531.87590.7688-0.99660.11350.00960.0516-0.0887-0.10820.192344.2809-4.5618-25.6681
46.2679-1.4424-1.626511.75360.57024.42570.34250.85460.7875-0.9029-0.57361.0504-0.3454-0.45520.23110.56030.1968-0.24280.03140.05690.310426.8331-4.9383-14.212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 1681 - 168
2X-RAY DIFFRACTION2AC169 - 240169 - 240
3X-RAY DIFFRACTION3AC241 - 344241 - 344
4X-RAY DIFFRACTION4PA1 - 101 - 10
5X-RAY DIFFRACTION4TB2 - 142 - 14

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