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

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Basic information

Entry
Database: PDB / ID: 4dqp
TitleTernary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (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
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / Cytosine-Guanine / 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',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 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 / 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_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*(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)149,92813
Polymers148,3336
Non-polymers1,5947
Water23,4561302
1
A: DNA polymerase
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)75,0936
Polymers74,1673
Non-polymers9273
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-25 kcal/mol
Surface area27500 Å2
MethodPISA
2
D: DNA polymerase
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)74,8347
Polymers74,1673
Non-polymers6684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-48 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.220, 109.340, 149.930
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


Mass: 67474.289 Da / Num. of mol.: 2 / Fragment: unp residues 287-878 / Mutation: D598A, 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

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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 / Details: DNA Primer Strand
#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 / Details: DNA Template Strand

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Non-polymers , 4 types, 1309 molecules

#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#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.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1302 / 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: 52.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 45%-53% 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: 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: 1.74→50 Å / Num. obs: 142490 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 28.907 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.74-1.840.494.361100
1.84-1.970.3395.95157.4
1.97-2.130.18310.161100
2.13-2.330.12713.61172.5
2.33-2.60.09217.641100
2.6-30.07620.461100
3-3.670.06124.78199.6
3.67-5.180.05328.4199.6
5.18-500.04730.79198.9

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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: 1.74→29.448 Å / Occupancy max: 1 / Occupancy min: 0.08 / SU ML: 0.17 / σ(F): 2.35 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 6153 4.46 %
Rwork0.1666 --
obs0.1679 138100 87.01 %
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--0.3568 Å2-0 Å20 Å2
2---1.2175 Å2-0 Å2
3---1.5743 Å2
Refinement stepCycle: LAST / Resolution: 1.74→29.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9259 850 93 1302 11504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210666
X-RAY DIFFRACTIONf_angle_d1.39514647
X-RAY DIFFRACTIONf_dihedral_angle_d16.534126
X-RAY DIFFRACTIONf_chiral_restr0.081635
X-RAY DIFFRACTIONf_plane_restr0.0071750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.75980.26022370.2074508X-RAY DIFFRACTION91
1.7598-1.78050.25192370.20634500X-RAY DIFFRACTION91
1.7805-1.80220.25182420.19554592X-RAY DIFFRACTION92
1.8022-1.8250.21832440.19314629X-RAY DIFFRACTION93
1.825-1.8490.24872430.18414628X-RAY DIFFRACTION93
1.849-1.87430.21932410.18554572X-RAY DIFFRACTION92
1.8743-1.90110.27291320.18862503X-RAY DIFFRACTION85
1.9295-1.95960.25321120.19282131X-RAY DIFFRACTION84
1.9596-1.99170.22382350.18384751X-RAY DIFFRACTION95
1.9917-2.02610.20521870.17174896X-RAY DIFFRACTION97
2.0261-2.06290.18361710.16844891X-RAY DIFFRACTION96
2.0629-2.10260.21441910.17274941X-RAY DIFFRACTION98
2.1026-2.14550.18912070.16314965X-RAY DIFFRACTION99
2.1455-2.19210.18391870.15875023X-RAY DIFFRACTION99
2.1921-2.24310.21771540.16512665X-RAY DIFFRACTION91
2.2431-2.29920.2245650.16521773X-RAY DIFFRACTION84
2.2992-2.36130.19181950.16395036X-RAY DIFFRACTION99
2.3613-2.43080.20062080.16224976X-RAY DIFFRACTION99
2.4308-2.50920.18692020.16235070X-RAY DIFFRACTION99
2.5092-2.59880.19822170.16495040X-RAY DIFFRACTION99
2.5988-2.70280.17972080.16845054X-RAY DIFFRACTION99
2.7028-2.82570.21092260.17665052X-RAY DIFFRACTION100
2.8257-2.97450.21072300.17365065X-RAY DIFFRACTION100
2.9745-3.16070.20552570.17345068X-RAY DIFFRACTION100
3.1607-3.40440.18022680.16295057X-RAY DIFFRACTION100
3.4044-3.74640.19322480.16024982X-RAY DIFFRACTION98
3.7464-4.28710.15462640.14085110X-RAY DIFFRACTION100
4.2871-5.39580.17752710.14225147X-RAY DIFFRACTION100
5.3958-29.45190.1952740.18755322X-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)
11.44060.7945-0.47421.202-0.43431.2058-0.09250.3273-0.2784-0.48210.0794-0.11270.2311-0.06980.03160.5520.03120.17350.2896-0.02150.3117118.4347-57.35922.8424
20.2505-0.11390.05172.5067-0.140.9872-0.034-0.15150.04230.17180.03130.0044-0.0940.13030.00050.2892-0.03280.05590.22240.01370.2036115.1835-32.056746.8971
32.3361-1.1986-0.16261.00040.11912.227-0.1229-0.63080.7915-0.45650.1321-0.8826-0.76560.4102-0.10490.6673-0.13590.2410.4228-0.01710.5726129.6314-15.981333.9467
41.08340.2433-0.27562.1932-0.67112.6770.0449-0.2521-0.0650.0066-0.2186-0.9318-0.36981.01940.27860.3283-0.08330.11660.55240.04590.4726134.4364-37.260141.4381
51.4883-0.25480.2991.63890.30611.32760.0250.0069-0.1146-0.04610.0156-0.04410.10490.0846-0.02440.07140.0242-0.01120.0811-0.02090.0723138.9373-47.7296-9.3171
60.6290.3795-0.07341.3925-0.52650.6623-0.10130.18240.1222-0.31940.20670.1943-0.0707-0.0827-0.08540.19630.0009-0.01360.1445-0.01310.1296123.2728-20.3477-30.3499
70.93810.016-0.10021.26010.58520.96860.03480.10420.1558-0.0752-0.05090.1217-0.1243-0.06020.0090.0580.00810.00680.0970.0110.1042119.0135-18.4546-8.4335
83.4107-0.3009-0.57332.78870.01123.3179-0.13320.0223-0.0391-0.5834-0.03410.4574-0.168-0.03920.13030.3625-0.005-0.00610.1615-0.05330.2922109.167-28.301940.1795
93.59150.6784-0.91682.92730.52381.5258-0.14760.13350.3574-0.57210.03960.5334-0.0956-0.13970.07990.33710.0265-0.00810.22690.03430.2575111.1166-27.063237.177
101.90021.0299-0.87241.0562-0.42293.3757-0.08760.12780.0797-0.11010.104-0.32860.05020.1509-0.07340.1690.02620.03030.14370.00220.2134130.5413-18.494-27.0666
110.9164-0.4739-0.51390.7439-0.31181.98830.10110.12630.2256-0.2780.0977-0.2285-0.23330.1406-0.19310.1508-0.02810.07130.1647-0.00130.1941131.9851-17.3214-23.7591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:467)
2X-RAY DIFFRACTION2chain 'A' and (resseq 468:666)
3X-RAY DIFFRACTION3chain 'A' and (resseq 667:780)
4X-RAY DIFFRACTION4chain 'A' and (resseq 781:876)
5X-RAY DIFFRACTION5chain 'D' and (resseq 298:467)
6X-RAY DIFFRACTION6chain 'D' and (resseq 468:604)
7X-RAY DIFFRACTION7chain 'D' and (resseq 605:876)
8X-RAY DIFFRACTION8chain 'B' and (resseq 21:29)
9X-RAY DIFFRACTION9chain 'C' and (resseq 1:12)
10X-RAY DIFFRACTION10chain 'E' and (resseq 21:29)
11X-RAY DIFFRACTION11chain 'F' and (resseq 1:12)

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