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

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Basic information

Entry
Database: PDB / ID: 3thv
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddATP-dT in Closed Conformation
Components
  • 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'
  • 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DA))-3'
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase I / protein-DNA complex / 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'-dideoxyadenosine triphosphate / DNA / DNA (> 10) / :
Similarity search - Component
Biological speciesGeobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.611 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*(2DA))-3'
C: 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DA))-3'
F: 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,60113
Polymers148,3136
Non-polymers1,2877
Water30,5531696
1
A: DNA polymerase I
B: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DA))-3'
C: 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7526
Polymers74,1573
Non-polymers5963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-39 kcal/mol
Surface area27440 Å2
MethodPISA
2
D: DNA polymerase I
E: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DA))-3'
F: 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8487
Polymers74,1573
Non-polymers6924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-50 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.810, 109.270, 150.430
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) / Mutation: D598A/F710Y
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*(2DA))-3'


Mass: 2659.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer Strand
#3: DNA chain 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'


Mass: 4006.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template Strand

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Non-polymers , 4 types, 1703 molecules

#4: Chemical ChemComp-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#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.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1696 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
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

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: 1.61→100 Å / Num. obs: 193977 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.61-1.710.4933.58191.4
1.71-1.830.2985.921100
1.83-1.970.2127.5194.9
1.97-2.160.11513.091100
2.16-2.420.08715.57194.8
2.42-2.790.06420.981100
2.79-3.420.0525.461100
3.42-4.830.04230.92199.2
4.83-1000.03337.26198.7

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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: 1.611→88.408 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.44 / σ(F): 2.35 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 8426 4.55 %
Rwork0.1933 --
obs0.1947 185284 93.02 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.838 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3738 Å2-0 Å20 Å2
2---1.2769 Å2-0 Å2
3---0.9031 Å2
Refinement stepCycle: LAST / Resolution: 1.611→88.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9293 846 75 1696 11910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110540
X-RAY DIFFRACTIONf_angle_d1.26614445
X-RAY DIFFRACTIONf_dihedral_angle_d15.5114082
X-RAY DIFFRACTIONf_chiral_restr0.0731611
X-RAY DIFFRACTIONf_plane_restr0.0061723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6111-1.62940.28771760.26453350X-RAY DIFFRACTION54
1.6294-1.64860.28042940.24455570X-RAY DIFFRACTION89
1.6486-1.66870.25632950.24475609X-RAY DIFFRACTION90
1.6687-1.68990.28292980.2325674X-RAY DIFFRACTION91
1.6899-1.71210.27093030.22045754X-RAY DIFFRACTION92
1.7121-1.73550.2563100.21745873X-RAY DIFFRACTION93
1.7355-1.76030.24633050.22145805X-RAY DIFFRACTION93
1.7603-1.78660.24893080.2245855X-RAY DIFFRACTION94
1.7866-1.81450.25413150.21185978X-RAY DIFFRACTION95
1.8145-1.84430.26023130.21115958X-RAY DIFFRACTION95
1.8443-1.87610.25413140.20945962X-RAY DIFFRACTION95
1.8761-1.91020.33352490.27314722X-RAY DIFFRACTION76
1.9102-1.9470.39322600.35794957X-RAY DIFFRACTION79
1.947-1.98670.24582990.20496015X-RAY DIFFRACTION96
1.9867-2.02990.21662180.18746258X-RAY DIFFRACTION98
2.0299-2.07710.20932180.1856227X-RAY DIFFRACTION98
2.0771-2.12910.22772570.18346328X-RAY DIFFRACTION99
2.1291-2.18660.20672370.17926321X-RAY DIFFRACTION99
2.1866-2.2510.29022750.25125289X-RAY DIFFRACTION85
2.251-2.32370.27061920.23265537X-RAY DIFFRACTION86
2.3237-2.40670.21252600.17446363X-RAY DIFFRACTION99
2.4067-2.50310.22272520.17666313X-RAY DIFFRACTION99
2.5031-2.6170.21042640.17556370X-RAY DIFFRACTION100
2.617-2.7550.20522750.17786338X-RAY DIFFRACTION99
2.755-2.92760.21892950.18396369X-RAY DIFFRACTION100
2.9276-3.15370.20743180.18356349X-RAY DIFFRACTION100
3.1537-3.4710.18933260.1716372X-RAY DIFFRACTION100
3.471-3.97330.18693200.16596267X-RAY DIFFRACTION98
3.9733-5.00590.18943370.15676473X-RAY DIFFRACTION100
5.0059-88.54130.21843430.20016602X-RAY DIFFRACTION98

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