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- PDB-4dqs: Binary complex of Bacillus DNA Polymerase I Large Fragment and du... -

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Basic information

Entry
Database: PDB / ID: 4dqs
TitleBinary complex of Bacillus DNA Polymerase I Large Fragment and duplex DNA with rC in primer terminus paired with dG of template
Components
  • DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA polymerase
  • DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3')
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / rC-dG / TRANSFERASE-DNA complex
Function / homology
Function and homology information


5'-3' exonuclease activity / 3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / 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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 ...: / DNA polymerase I, ribonuclease H-like domain / 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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease domain / 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
CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.66 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 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3')
C: DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7806
Polymers76,1053
Non-polymers6753
Water15,439857
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-41 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.410, 93.410, 105.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein / DNA/RNA hybrid / DNA chain , 3 types, 3 molecules ABC

#1: Protein DNA polymerase


Mass: 67518.297 Da / Num. of mol.: 1 / Fragment: un residues 287-878 / Mutation: H539R
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/RNA hybrid DNA/RNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-R(P*C)-3')


Mass: 3663.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Primer Strand
#3: DNA chain DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 4923.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Template Strand

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Non-polymers , 3 types, 860 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 44%-49% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MnSO4, 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: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.66→100 Å / Num. obs: 103591 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 28.649 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.18
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.66-1.760.4893.34199.9
1.76-1.880.285.741100
1.88-2.030.1510.23199.8
2.03-2.220.07917.71199.9
2.22-2.480.05325.62199.4
2.48-2.870.03733.31199.9
2.87-3.510.02645.15199.9
3.51-4.950.0257.19199.8
4.95-1000.01763.57197.9

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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 1L5U

1l5u


Resolution: 1.66→45.382 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.13 / σ(F): 1.99 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1808 5031 4.86 %
Rwork0.1604 --
obs0.1614 103589 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.2036 Å2-0 Å2-0 Å2
2---3.1548 Å20 Å2
3----2.0488 Å2
Refinement stepCycle: LAST / Resolution: 1.66→45.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 468 39 857 5964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015336
X-RAY DIFFRACTIONf_angle_d1.2917338
X-RAY DIFFRACTIONf_dihedral_angle_d16.332074
X-RAY DIFFRACTIONf_chiral_restr0.071826
X-RAY DIFFRACTIONf_plane_restr0.006871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.67890.25721710.24663252X-RAY DIFFRACTION100
1.6789-1.69860.24121720.23013258X-RAY DIFFRACTION100
1.6986-1.71930.2271690.21393220X-RAY DIFFRACTION100
1.7193-1.74110.23041710.20713243X-RAY DIFFRACTION100
1.7411-1.7640.20381720.19533272X-RAY DIFFRACTION100
1.764-1.78820.21931710.19353258X-RAY DIFFRACTION100
1.7882-1.81370.23011720.18853258X-RAY DIFFRACTION100
1.8137-1.84080.22911700.18213241X-RAY DIFFRACTION100
1.8408-1.86960.20941720.1853261X-RAY DIFFRACTION100
1.8696-1.90020.2481700.18863222X-RAY DIFFRACTION100
1.9002-1.9330.28791720.2233281X-RAY DIFFRACTION99
1.933-1.96810.19431320.17313279X-RAY DIFFRACTION100
1.9681-2.0060.1791280.17363302X-RAY DIFFRACTION100
2.006-2.04690.17561360.15643312X-RAY DIFFRACTION100
2.0469-2.09150.17811490.15483267X-RAY DIFFRACTION100
2.0915-2.14010.16861700.14973290X-RAY DIFFRACTION100
2.1401-2.19360.18071700.14933276X-RAY DIFFRACTION100
2.1936-2.25290.18671630.16533244X-RAY DIFFRACTION99
2.2529-2.31920.17051900.14873213X-RAY DIFFRACTION99
2.3192-2.39410.14361740.14563285X-RAY DIFFRACTION100
2.3941-2.47960.17461840.14343270X-RAY DIFFRACTION100
2.4796-2.57890.18391730.14573303X-RAY DIFFRACTION100
2.5789-2.69630.18471620.15653301X-RAY DIFFRACTION100
2.6963-2.83840.16781880.15553276X-RAY DIFFRACTION100
2.8384-3.01620.18521630.15793329X-RAY DIFFRACTION100
3.0162-3.2490.18831510.16253320X-RAY DIFFRACTION100
3.249-3.57590.17721890.1433329X-RAY DIFFRACTION100
3.5759-4.0930.14931680.13743344X-RAY DIFFRACTION100
4.093-5.15560.13931640.13313414X-RAY DIFFRACTION100
5.1556-45.39870.1941950.19013438X-RAY DIFFRACTION98
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)
11.69160.6817-0.45871.53440.011.024-0.09060.2526-0.1469-0.21480.0482-0.07840.1077-0.03990.02570.1298-0.00540.01610.1456-0.01630.11449.543825.9025.872
20.3472-0.2585-0.49961.0864-0.32191.34050.0151-0.23890.19540.1166-0.1375-0.1999-0.10010.42850.06180.0878-0.0262-0.00430.23270.04420.111123.997143.471725.1647
30.5001-0.56981.33031.0756-0.03672.09280.06810.07710.03120.46750.1016-0.10420.72910.63-0.04050.50290.137-0.05260.42270.03110.260436.120737.745739.4699
40.5975-0.0339-0.04930.71950.07340.65150.0269-0.06690.0140.1079-0.0267-0.07710.03780.01690.0050.1116-0.0138-0.00540.11650.00410.13547.923644.585235.9732
55.6544-1.15392.19926.90642.0265.7040.01850.9779-0.0946-0.6227-0.0299-0.26130.2953-0.1820.18761.56140.39060.07670.9026-0.3591.053431.065720.317225.8
66.6924-2.77181.09025.3789-0.56923.5724-0.06340.0228-0.39290.5510.0055-0.15430.70030.39480.12040.39530.0328-0.02310.28480.02490.228624.384335.736236.9031
71.5938-0.34220.85952.24950.86920.9801-0.1619-0.26860.00830.4490.0673-0.31360.54740.41230.12890.29710.0443-0.03480.30220.05940.254221.578933.513433.4713
85.0173-2.0482-1.84093.26671.8682.0706-0.2146-0.0193-1.41810.4520.00410.28911.08940.205-0.05721.60830.8321-0.29190.4955-0.24910.714736.579821.105733.2135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 298:467)
2X-RAY DIFFRACTION2chain 'A' and (resseq 468:522)
3X-RAY DIFFRACTION3chain 'A' and (resseq 523:604)
4X-RAY DIFFRACTION4chain 'A' and (resseq 605:876)
5X-RAY DIFFRACTION5chain 'B' and (resseq 18:22)
6X-RAY DIFFRACTION6chain 'B' and (resseq 23:29)
7X-RAY DIFFRACTION7chain 'C' and (resseq 3:10)
8X-RAY DIFFRACTION8chain 'C' and (resseq 11:16)

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