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- PDB-3ti0: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -

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Basic information

Entry
Database: PDB / ID: 3ti0
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddGTP-dC in Closed Conformation
Components
  • 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
  • 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase I / protein-DNA complex / guanine-cytosine / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / :
Similarity search - Component
Biological speciesGeobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.62 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structures of mismatch replication errors observed in a DNA polymerase.
Authors: Johnson, S.J. / Beese, L.S.
History
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Sep 13, 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_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_asym_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_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 I
D: DNA polymerase I
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
F: 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,50812
Polymers148,2856
Non-polymers1,2236
Water30,3911687
1
A: DNA polymerase I
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
C: 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7546
Polymers74,1433
Non-polymers6123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-33 kcal/mol
Surface area27230 Å2
MethodPISA
2
D: DNA polymerase I
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'
F: 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7546
Polymers74,1433
Non-polymers6123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-36 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 108.920, 149.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase I


Mass: 67490.289 Da / Num. of mol.: 2 / Fragment: Bacillus Fragment (UNP residues 285-876)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C9RTX7, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer Strand
#3: DNA chain 5'-D(*C*AP*TP*CP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'


Mass: 3976.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template Strand

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Non-polymers , 4 types, 1693 molecules

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


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1687 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT THE GEOBACILLUS SP. STRAIN IS UNKNOWN BUT SIMILAR TO Y412MC61.

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 45-50% saturated ammonium sulfate, 2.5% MPD, 10 mM magnesium sulfate, 100 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97121 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2009
RadiationMonochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 1.62→100 Å / Num. obs: 190278 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.62-1.710.4933.46199.6
1.71-1.830.3045.551100
1.83-1.980.2356.44195.5
1.98-2.170.12111.891100
2.17-2.420.09813.16195.7
2.42-2.80.07317.8199.6
2.8-3.430.05821.49199.1
3.43-4.840.0525.57197.4
4.84-1000.03831.72195.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2HVI

2hvi


Resolution: 1.62→42.96 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.45 / σ(F): 2.35 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 8204 4.54 %
Rwork0.1866 --
obs0.1879 180731 93.36 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.407 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5157 Å2-0 Å20 Å2
2---2.1747 Å2-0 Å2
3---0.6589 Å2
Refinement stepCycle: LAST / Resolution: 1.62→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9293 844 72 1687 11896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810523
X-RAY DIFFRACTIONf_angle_d1.22114420
X-RAY DIFFRACTIONf_dihedral_angle_d15.2024075
X-RAY DIFFRACTIONf_chiral_restr0.0651610
X-RAY DIFFRACTIONf_plane_restr0.0061719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.30762700.2555140X-RAY DIFFRACTION85
1.6384-1.65770.28552860.24215421X-RAY DIFFRACTION89
1.6577-1.67790.28762870.23865469X-RAY DIFFRACTION90
1.6779-1.69910.27582890.22885490X-RAY DIFFRACTION90
1.6991-1.72150.24152910.21215518X-RAY DIFFRACTION91
1.7215-1.74510.25482960.21125623X-RAY DIFFRACTION92
1.7451-1.770.25672950.21195609X-RAY DIFFRACTION92
1.77-1.79640.24563020.20015738X-RAY DIFFRACTION94
1.7964-1.82450.23962990.20525690X-RAY DIFFRACTION94
1.8245-1.85440.24463000.20035696X-RAY DIFFRACTION94
1.8544-1.88640.24232980.20685648X-RAY DIFFRACTION93
1.8864-1.92070.39642340.35344477X-RAY DIFFRACTION73
1.9207-1.95760.27892560.23434866X-RAY DIFFRACTION80
1.9576-1.99760.23982550.18945900X-RAY DIFFRACTION96
1.9976-2.0410.20282120.17936059X-RAY DIFFRACTION98
2.041-2.08850.20172240.17596064X-RAY DIFFRACTION98
2.0885-2.14070.18812450.17636095X-RAY DIFFRACTION98
2.1407-2.19860.21712570.17716022X-RAY DIFFRACTION98
2.1986-2.26330.27762170.25514975X-RAY DIFFRACTION80
2.2633-2.33640.22992240.17965814X-RAY DIFFRACTION94
2.3364-2.41990.20862530.16876082X-RAY DIFFRACTION99
2.4199-2.51670.21032400.16936137X-RAY DIFFRACTION99
2.5167-2.63130.20742540.17536147X-RAY DIFFRACTION99
2.6313-2.770.21522710.17416130X-RAY DIFFRACTION99
2.77-2.94350.20162800.17736125X-RAY DIFFRACTION99
2.9435-3.17070.19753070.1776098X-RAY DIFFRACTION99
3.1707-3.48960.18823190.16846135X-RAY DIFFRACTION99
3.4896-3.99430.17753070.16625974X-RAY DIFFRACTION96
3.9943-5.03110.18873150.15396166X-RAY DIFFRACTION98
5.0311-42.97510.19643210.19586219X-RAY DIFFRACTION95

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