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- PDB-4dqi: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA ... -

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Basic information

Entry
Database: PDB / ID: 4dqi
TitleTernary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and dCTP (paired with dG of template)
Components
  • DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / Cytosine-Guanine / closed form / TRANSFERASE-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / 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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
Authors: Wang, W. / Wu, E.Y. / Hellinga, H.W. / Beese, L.S.
#1: 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.
History
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Database references
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 / 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_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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*(DOC))-3')
C: DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,97613
Polymers148,3336
Non-polymers1,6427
Water29,4731636
1
A: DNA polymerase I
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2217
Polymers74,1673
Non-polymers1,0554
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-33 kcal/mol
Surface area27450 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7546
Polymers74,1673
Non-polymers5883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-38 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.680, 109.360, 150.320
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: 67474.289 Da / Num. of mol.: 2
Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment)
Mutation: D598A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK2730, GYMC61_0787, polA / 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*(DOC))-3')


Mass: 2635.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*C*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4056.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 4 types, 1643 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#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.: 1636 / 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 THESE RESIDUES.

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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: 52.61 %
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

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 155734 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 26.719 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.69-1.790.4913.29194.9
1.79-1.910.3294.97186.1
1.91-2.070.1748.52177.7
2.07-2.260.12311.85182.9
2.26-2.530.08416.33192.9
2.53-2.920.06420.47199.5
2.92-3.570.04726.42198.7
3.57-5.030.0432.32196.2
5.03-500.03337.81194.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1026refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2HVI

2hvi


Resolution: 1.69→28.768 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.16 / σ(F): 2.35 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 6645 4.48 %Inherited free reflections from 2HVI plus randomly generated reflections beyond 1.98A resolution
Rwork0.1582 ---
obs0.1594 148420 86.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å20 Å2
2---1.2794 Å2-0 Å2
3---2.0994 Å2
Refinement stepCycle: LAST / Resolution: 1.69→28.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 850 96 1636 11874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110795
X-RAY DIFFRACTIONf_angle_d1.34714835
X-RAY DIFFRACTIONf_dihedral_angle_d15.3884205
X-RAY DIFFRACTIONf_chiral_restr0.0761652
X-RAY DIFFRACTIONf_plane_restr0.0071786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.70920.26471750.24443335X-RAY DIFFRACTION62
1.7092-1.72930.25322520.20824785X-RAY DIFFRACTION89
1.7293-1.75040.25232570.19994873X-RAY DIFFRACTION89
1.7504-1.77250.2522540.20084825X-RAY DIFFRACTION89
1.7725-1.79590.23222600.18824950X-RAY DIFFRACTION91
1.7959-1.82050.21722610.17794961X-RAY DIFFRACTION92
1.8205-1.84650.23282620.17554971X-RAY DIFFRACTION92
1.8465-1.8740.21182640.17115021X-RAY DIFFRACTION92
1.874-1.90330.17161560.17062962X-RAY DIFFRACTION76
1.9033-1.93450.535810.32994X-RAY DIFFRACTION1
1.9345-1.96790.2231990.17423788X-RAY DIFFRACTION70
1.9679-2.00360.20352060.16815265X-RAY DIFFRACTION96
2.0036-2.04220.17571890.15445322X-RAY DIFFRACTION96
2.0422-2.08380.17751860.15285317X-RAY DIFFRACTION96
2.0838-2.12910.15532190.14875330X-RAY DIFFRACTION97
2.1291-2.17860.18242080.15075383X-RAY DIFFRACTION97
2.1786-2.23310.18442130.16094162X-RAY DIFFRACTION85
2.2331-2.29350.2556490.1751412X-RAY DIFFRACTION52
2.2935-2.36090.16912140.15035420X-RAY DIFFRACTION98
2.3609-2.43710.1832240.14645411X-RAY DIFFRACTION99
2.4371-2.52410.17962190.14815475X-RAY DIFFRACTION99
2.5241-2.62510.16542280.15395417X-RAY DIFFRACTION98
2.6251-2.74450.18192320.16045440X-RAY DIFFRACTION98
2.7445-2.88910.19422500.16145471X-RAY DIFFRACTION99
2.8891-3.06990.20232650.16525414X-RAY DIFFRACTION98
3.0699-3.30660.18082790.15525442X-RAY DIFFRACTION98
3.3066-3.63880.16712760.14255337X-RAY DIFFRACTION96
3.6388-4.1640.15272770.14185299X-RAY DIFFRACTION95
4.164-5.2410.16782820.13465443X-RAY DIFFRACTION97
5.241-28.77210.19012880.18185540X-RAY DIFFRACTION95
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)
10.92880.3254-0.06161.5511.0952.0504-0.11060.2077-0.2549-0.3186-0.0731-0.01320.4118-0.17270.14060.43130.02430.08750.2007-0.0070.2304116.6361-64.16423.2925
20.62620.4569-0.40071.6717-0.21651.2469-0.03150.059-0.1555-0.2099-0.0942-0.17210.23810.15870.07660.2770.06560.07470.20740.03270.2074122.5368-56.592327.8984
32.90481.2095-1.91962.2029-0.59591.9408-0.02730.56650.4169-0.24480.05160.4715-0.1591-0.2875-0.04450.30920.0473-0.05040.31630.08090.3042107.6247-50.802819.5293
40.62150.0811-0.38611.1285-0.24630.6242-0.07130.1218-0.0586-0.2643-0.002-0.1770.12670.08090.04890.2630.03360.07330.220.03950.1933123.9703-50.324224.3025
50.8976-1.3450.32053.3236-0.96470.494-0.0871-0.1307-0.10150.580.1470.3689-0.1681-0.0941-0.05240.3551-0.02070.05740.2077-0.00640.245101.8878-26.611256.8899
61.0110.26170.44991.48470.76572.113-0.01180.0319-0.0077-0.13840.19140.081-0.1443-0.0038-0.12690.2949-0.0184-0.02560.15750.00250.2314102.7322-12.035544.9302
70.6872-0.3247-0.13571.3058-0.0161.2984-0.0074-0.11160.07480.2183-0.0802-0.205-0.03980.27650.03630.1863-0.0467-0.0360.21840.03630.1693121.9907-34.160446.0244
81.18050.1331-0.13682.16210.02031.80960.2016-0.24780.23480.0409-0.2484-0.4087-0.49180.12830.04830.3443-0.08010.04340.28330.01370.3132128.7272-16.103833.6409
90.40380.2663-0.39771.16250.22911.56070.0246-0.13280.00660.1672-0.2089-0.6286-0.03430.53750.06220.1687-0.0264-0.01510.36550.09420.3414133.9913-37.127340.9802
101.1021-0.1760.30391.17590.32461.2005-0.0087-0.0067-0.0725-0.03880.0109-0.03970.09020.09140.00970.060.0278-0.00370.0679-0.00710.06138.1013-47.7872-9.2372
110.43380.1622-0.00790.9574-0.33420.6421-0.0460.12010.0699-0.20670.13010.0891-0.0865-0.0429-0.07950.13930.00170.00040.0956-0.00430.0938122.2923-20.3921-31.127
120.83730.08820.04150.94280.49680.8560.01970.09590.1557-0.0602-0.03860.0922-0.1164-0.05010.00010.04340.01130.00390.07590.02080.0922118.2579-18.6646-8.7393
131.36680.1032-0.3490.4284-0.15551.658-0.10310.0625-0.099-0.3399-0.02660.2927-0.058-0.10450.11740.2657-0.0286-0.070.1817-0.05980.2546108.6374-28.224740.1774
141.88440.2061-0.53771.42610.50470.8731-0.04480.06820.1487-0.2393-0.02540.279-0.0513-0.08910.03610.18850.0096-0.02720.17520.0150.1666110.5193-27.087737.2025
151.46160.4629-0.67940.6212-0.01021.6124-0.01230.01970.1314-0.08080.0987-0.17410.01140.0955-0.08310.120.02150.01860.1015-0.00130.1342129.6692-18.5973-27.2176
160.7352-0.3725-0.40580.3605-0.20021.20280.07610.130.1372-0.23130.0755-0.2725-0.16030.0412-0.1410.1253-0.02220.05920.12370.01260.1295131.1205-17.4809-23.9231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 298:347)
2X-RAY DIFFRACTION2chain 'A' and (resseq 348:409)
3X-RAY DIFFRACTION3chain 'A' and (resseq 410:439)
4X-RAY DIFFRACTION4chain 'A' and (resseq 440:496)
5X-RAY DIFFRACTION5chain 'A' and (resseq 497:539)
6X-RAY DIFFRACTION6chain 'A' and (resseq 540:568)
7X-RAY DIFFRACTION7chain 'A' and (resseq 569:676)
8X-RAY DIFFRACTION8chain 'A' and (resseq 677:780)
9X-RAY DIFFRACTION9chain 'A' and (resseq 781:876)
10X-RAY DIFFRACTION10chain 'D' and (resseq 298:467)
11X-RAY DIFFRACTION11chain 'D' and (resseq 468:604)
12X-RAY DIFFRACTION12chain 'D' and (resseq 605:876)
13X-RAY DIFFRACTION13chain 'B' and (resseq 21:29)
14X-RAY DIFFRACTION14chain 'C' and (resseq 1:12)
15X-RAY DIFFRACTION15chain 'E' and (resseq 21:29)
16X-RAY DIFFRACTION16chain 'F' and (resseq 1:12)

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