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- PDB-3pv8: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -

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Basic information

Entry
Database: PDB / ID: 3pv8
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation
Components
  • DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / Thymine-Adenine / closed conformation / TRANSFERASE-DNA complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / DNA binding / metal ion binding
Similarity search - Function
DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 ...DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsWang, W. / Beese, L.S.
CitationJournal: 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.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Jan 11, 2017Group: Other
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 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_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_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
C: DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
F: DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,60113
Polymers148,3316
Non-polymers1,2697
Water32,8411823
1
A: DNA polymerase I
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
C: DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7526
Polymers74,1663
Non-polymers5873
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-36 kcal/mol
Surface area27570 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
F: DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8487
Polymers74,1663
Non-polymers6834
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-49 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.890, 109.300, 150.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (analogous to E. coli Klenow Fragment)
Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2650.762 Da / Num. of mol.: 2 / Fragment: DNA primer strand / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*C*AP*TP*AP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4024.649 Da / Num. of mol.: 2 / Fragment: DNA template strand / Source method: obtained synthetically

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Non-polymers , 4 types, 1830 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1823 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE.

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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: 52.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium Sulfate, MPD, MgSO4, MES, pH 5.8, vapor diffusion, hanging drop, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2MPD11
3MgSO411
4MES11
5Ammonium Sulfate12
6MPD12
7MgSO412
8MES12

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 1.52→100 Å / Num. obs: 231085 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.52-1.610.4924.2195.4
1.61-1.720.3116.7198.2
1.72-1.860.1919.7198.6
1.86-2.030.1412.3195
2.03-2.270.09217.2196.7
2.27-2.630.0721.3198.9
2.63-3.220.05725.7199.7
3.22-4.540.04930.8199.4
4.54-1000.03638.4197.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2HVI with insertion site base pair, metal ions, and protein residues 681-727 deleted.

2hvi


Resolution: 1.52→88.422 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.36 / σ(F): 2.35 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 10319 4.64 %
Rwork0.1853 --
obs0.1865 222603 93.91 %
all-237031 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.623 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7489 Å2-0 Å2-0 Å2
2---1.2945 Å20 Å2
3----0.4544 Å2
Refinement stepCycle: LAST / Resolution: 1.52→88.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9289 848 73 1823 12033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910543
X-RAY DIFFRACTIONf_angle_d1.24514455
X-RAY DIFFRACTIONf_dihedral_angle_d15.2814085
X-RAY DIFFRACTIONf_chiral_restr0.0671615
X-RAY DIFFRACTIONf_plane_restr0.0061724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.53730.25913120.24355935X-RAY DIFFRACTION80
1.5373-1.55540.25963370.23016405X-RAY DIFFRACTION86
1.5554-1.57430.27493500.22476643X-RAY DIFFRACTION90
1.5743-1.59430.24673540.21796729X-RAY DIFFRACTION90
1.5943-1.61520.22513580.20886790X-RAY DIFFRACTION91
1.6152-1.63740.24363580.20726804X-RAY DIFFRACTION92
1.6374-1.66080.22793650.19756948X-RAY DIFFRACTION93
1.6608-1.68560.22333660.19346949X-RAY DIFFRACTION93
1.6856-1.71190.2283670.18876979X-RAY DIFFRACTION93
1.7119-1.740.22633690.18717010X-RAY DIFFRACTION94
1.74-1.770.25193710.18997038X-RAY DIFFRACTION95
1.77-1.80220.21833750.18527130X-RAY DIFFRACTION96
1.8022-1.83680.23713750.18457131X-RAY DIFFRACTION96
1.8368-1.87430.2273760.18157136X-RAY DIFFRACTION95
1.8743-1.91510.25243250.20436184X-RAY DIFFRACTION83
1.9151-1.95960.28253370.26266402X-RAY DIFFRACTION86
1.9596-2.00860.21393190.17897287X-RAY DIFFRACTION97
2.0086-2.0630.20052620.17227462X-RAY DIFFRACTION98
2.063-2.12370.18932990.17187423X-RAY DIFFRACTION98
2.1237-2.19220.18582880.17117471X-RAY DIFFRACTION98
2.1922-2.27060.24543130.22746503X-RAY DIFFRACTION87
2.2706-2.36150.20472700.16877319X-RAY DIFFRACTION96
2.3615-2.4690.20823130.1717495X-RAY DIFFRACTION99
2.469-2.59920.19393140.17067520X-RAY DIFFRACTION99
2.5992-2.7620.19223190.17887556X-RAY DIFFRACTION99
2.762-2.97530.22363520.18467558X-RAY DIFFRACTION99
2.9753-3.27470.20023840.18257559X-RAY DIFFRACTION99
3.2747-3.74860.18223880.16797537X-RAY DIFFRACTION99
3.7486-4.72280.17353990.16177647X-RAY DIFFRACTION99
4.7228-88.57170.22824040.20377734X-RAY DIFFRACTION97

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