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- PDB-4ds5: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA ... -

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Basic information

Entry
Database: PDB / ID: 4ds5
TitleTernary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+
Components
  • DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')
  • DNA polymerase
KeywordsTransferase/DNA / DNA Polymerase I / Transferase-DNA complex
Function / homology
Function and homology information


5'-3' exonuclease activity / 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
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 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 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 21, 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 / 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 / _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
D: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')
C: DNA (5'-D(*CP*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*C)-3')
F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,6549
Polymers148,3656
Non-polymers2883
Water20,1411118
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')
C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)74,1833
Polymers74,1833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-24 kcal/mol
Surface area27510 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')
F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4716
Polymers74,1833
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-34 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.880, 108.860, 150.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase


Mass: 67474.289 Da / Num. of mol.: 2 / Fragment: unp residues 287-878 / Mutation: D598A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')


Mass: 2651.750 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Primer Strand
#3: DNA chain DNA (5'-D(*CP*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 / Details: DNA Template Strand
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O
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: 52.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.68→100 Å / Num. obs: 157642 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 31.682 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.08
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.68-1.780.4664.15197.2
1.78-1.90.4496.83191.2
1.9-2.050.24913.12164.1
2.05-2.250.15518.77187.1
2.25-2.520.09426.46186.1
2.52-2.90.06832.33199.1
2.9-3.550.04937.67199.4
3.55-5.020.04340.62198.8
5.02-1000.03446.07199.3

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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 4DS4

4ds4


Resolution: 1.68→54.43 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.16 / σ(F): 2.35 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 6639 4.36 %
Rwork0.1758 --
obs0.1768 152367 86.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6132 Å20 Å2-0 Å2
2--0.1873 Å20 Å2
3----0.8004 Å2
Refinement stepCycle: LAST / Resolution: 1.68→54.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9145 772 15 1118 11050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110285
X-RAY DIFFRACTIONf_angle_d1.34514080
X-RAY DIFFRACTIONf_dihedral_angle_d14.7593960
X-RAY DIFFRACTIONf_chiral_restr0.0771581
X-RAY DIFFRACTIONf_plane_restr0.0071698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69910.31011330.24884874X-RAY DIFFRACTION87
1.6991-1.71910.24082400.22834836X-RAY DIFFRACTION88
1.7191-1.740.28852420.22214897X-RAY DIFFRACTION88
1.74-1.76210.25792450.21384968X-RAY DIFFRACTION90
1.7621-1.78530.24952450.20854978X-RAY DIFFRACTION90
1.7853-1.80970.21892600.19775052X-RAY DIFFRACTION91
1.8097-1.83560.21862540.19235120X-RAY DIFFRACTION92
1.8356-1.8630.21872510.18785057X-RAY DIFFRACTION92
1.863-1.89210.24182440.18894868X-RAY DIFFRACTION88
1.9231-1.95630.2575720.18821387X-RAY DIFFRACTION81
1.9563-1.99180.23352370.18515122X-RAY DIFFRACTION92
1.9918-2.03020.20181970.17715404X-RAY DIFFRACTION96
2.0302-2.07160.19041960.16875418X-RAY DIFFRACTION96
2.0716-2.11660.18352190.17025464X-RAY DIFFRACTION97
2.1166-2.16590.1812230.16775444X-RAY DIFFRACTION97
2.1659-2.22010.21012440.16995368X-RAY DIFFRACTION95
2.2201-2.28010.1622180.1875367X-RAY DIFFRACTION7
2.2801-2.34720.18052040.16515440X-RAY DIFFRACTION97
2.3472-2.42290.21042290.16055549X-RAY DIFFRACTION98
2.4229-2.50950.19182240.16925543X-RAY DIFFRACTION98
2.5095-2.610.16462360.17435544X-RAY DIFFRACTION98
2.61-2.72880.19952410.17975557X-RAY DIFFRACTION99
2.7288-2.87260.22922560.18995579X-RAY DIFFRACTION99
2.8726-3.05260.2252700.18615553X-RAY DIFFRACTION99
3.0526-3.28830.18042890.17575591X-RAY DIFFRACTION99
3.2883-3.61910.17422900.16195598X-RAY DIFFRACTION99
3.6191-4.14270.17692780.15785542X-RAY DIFFRACTION98
4.1427-5.21870.19073000.15075715X-RAY DIFFRACTION100
5.2187-54.45860.20733020.20125893X-RAY DIFFRACTION99
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)
11.85540.4168-0.07562.21780.62862.10540.0520.3617-0.4560.28050.0083-0.0241.0920.0927-0.04970.73020.08050.0210.346-0.04480.3796116.655-64.248923.6756
22.36211.35670.04642.69220.38461.6733-0.06720.53-0.13740.09170.1780.15520.43550.2674-0.09710.44090.10420.03450.35520.01960.2482118.2513-53.08821.9862
30.5104-0.09480.03531.7624-0.34582.0474-0.0847-0.16220.08970.52190.10140.3038-0.09360.0243-0.01910.3656-0.04080.03260.2247-0.00630.3042109.8564-29.767848.1728
41.34760.1306-0.12811.53070.35261.0306-0.0534-0.25420.09880.33820.0921-0.22530.08650.75110.01120.3463-0.0201-0.0470.5020.01420.2284128.1412-32.57942.4459
53.0134-0.06152.01571.4685-0.33221.4272-0.1899-1.15920.5430.44580.2218-0.3138-0.70750.2584-0.01210.6144-0.1248-0.03070.7909-0.1890.4659129.6952-9.238840.2568
60.90760.4992-0.69811.23150.28342.3336-0.032-0.1833-0.01090.1777-0.0244-0.33280.03080.81030.08440.22760.0008-0.03330.54080.02640.2605131.9091-32.254234.5908
71.7793-0.44920.35151.88070.70871.50950.06570.0018-0.1997-0.10640.0297-0.08950.15010.1035-0.05140.10920.0221-0.01070.0843-0.01820.1215137.9977-47.7549-9.4145
80.67160.4578-0.42551.2709-0.41990.4847-0.11380.28080.2098-0.43630.24780.1149-0.0697-0.1966-0.11050.3134-0.0324-0.02570.22260.04020.1818123.2682-17.8501-30.9363
91.2832-0.1763-0.11251.29850.6441.31840.04820.12730.2386-0.1815-0.06290.0305-0.1832-0.05890.02550.07460.00750.00380.09360.02120.1263118.8224-20.5129-9.525
106.2277-0.7780.1191.8954-0.64513.758-0.55220.05450.3488-0.36710.26610.3723-0.20630.02550.26550.3728-0.0309-0.04020.1811-0.03330.3411108.5081-28.050440.2105
111.3939-0.7641-0.05051.66420.81481.34480.03660.00710.4848-0.18680.03730.6351-0.0971-0.0698-0.10010.2885-0.0136-0.00090.22930.04020.4053109.8265-28.00638.0272
122.74661.4435-1.56261.0083-0.64154.4977-0.00080.35410.45-0.21090.1781-0.3701-0.0157-0.0614-0.20860.28950.04670.05720.18860.03950.3177129.8093-18.4848-27.212
131.0402-0.0241-0.55740.7044-1.07961.99170.08630.24520.1393-0.55230.0954-0.3287-0.35190.0775-0.27460.2872-0.02690.08510.23320.00510.1914130.5538-21.3903-26.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:354)
2X-RAY DIFFRACTION2chain 'A' and (resseq 355:467)
3X-RAY DIFFRACTION3chain 'A' and (resseq 468:604)
4X-RAY DIFFRACTION4chain 'A' and (resseq 605:676)
5X-RAY DIFFRACTION5chain 'A' and (resseq 677:743)
6X-RAY DIFFRACTION6chain 'A' and (resseq 744:876)
7X-RAY DIFFRACTION7chain 'D' and (resseq 296:467)
8X-RAY DIFFRACTION8chain 'D' and (resseq 468:586)
9X-RAY DIFFRACTION9chain 'D' and (resseq 587:876)
10X-RAY DIFFRACTION10chain 'B' and (resseq 21:29)
11X-RAY DIFFRACTION11chain 'C' and (resseq 2:12)
12X-RAY DIFFRACTION12chain 'E' and (resseq 21:29)
13X-RAY DIFFRACTION13chain 'F' and (resseq 1:12)

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