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- PDB-4dsf: Ternary complex of Bacillus DNA Polymerase I Large Fragment F710Y... -

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Basic information

Entry
Database: PDB / ID: 4dsf
TitleTernary complex of Bacillus DNA Polymerase I Large Fragment F710Y, DNA duplex, and rCTP (paired with dG of template) in presence of Mn2+
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*(DOC))-3')
  • DNA polymerase
KeywordsTransferase/DNA / DNA Polymerase I / 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 / 3'-5' exonuclease / 5'-3' exonuclease, C-terminal domain superfamily / 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 polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.661 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 18, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _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(*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*(DOC))-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)149,23311
Polymers148,3656
Non-polymers8675
Water21,0421168
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-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 area4600 Å2
ΔGint-25 kcal/mol
Surface area27150 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-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)75,0508
Polymers74,1833
Non-polymers8675
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-53 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.680, 109.060, 150.090
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: 67490.289 Da / Num. of mol.: 2 / Fragment: un residues 287-878 / Mutation: D598A, F710Y
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(*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

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Non-polymers , 3 types, 1173 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.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1168 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% 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: 1.1159 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: 1.66→100 Å / Num. obs: 164320 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 31.537 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.66-1.760.4913.62193.4
1.76-1.880.31261100
1.88-2.030.23410.89162.9
2.03-2.230.14317.35195.8
2.23-2.490.09124.17179.5
2.49-2.870.06929.841100
2.87-3.510.05135.131100
3.51-4.950.04339.63198.7
4.95-1000.03545.1198.9

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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: 4DSE

4dse


Resolution: 1.661→71.063 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.15 / σ(F): 2.35 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 6763 4.32 %
Rwork0.1771 --
obs0.1781 156479 86.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0014 Å20 Å2-0 Å2
2--0.5517 Å20 Å2
3----0.5531 Å2
Refinement stepCycle: LAST / Resolution: 1.661→71.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9021 790 49 1168 11028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110201
X-RAY DIFFRACTIONf_angle_d1.37913973
X-RAY DIFFRACTIONf_dihedral_angle_d14.7983938
X-RAY DIFFRACTIONf_chiral_restr0.0791563
X-RAY DIFFRACTIONf_plane_restr0.0071676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6612-1.68010.2481600.23223648X-RAY DIFFRACTION63
1.6801-1.69990.25492450.22335016X-RAY DIFFRACTION88
1.6999-1.72060.24552510.20845026X-RAY DIFFRACTION89
1.7206-1.74240.23942420.20655143X-RAY DIFFRACTION90
1.7424-1.76530.24012460.19795144X-RAY DIFFRACTION90
1.7653-1.78950.20642670.18845228X-RAY DIFFRACTION92
1.7895-1.81510.2142600.19185196X-RAY DIFFRACTION92
1.8151-1.84220.24472630.19155307X-RAY DIFFRACTION92
1.8422-1.8710.21812630.18655208X-RAY DIFFRACTION91
1.871-1.90160.24931130.19453300X-RAY DIFFRACTION76
1.9344-1.96960.22081980.18693815X-RAY DIFFRACTION77
1.9696-2.00750.20581890.18145579X-RAY DIFFRACTION97
2.0075-2.04850.19531970.17325641X-RAY DIFFRACTION97
2.0485-2.0930.17832110.17025683X-RAY DIFFRACTION98
2.093-2.14170.1822320.16755657X-RAY DIFFRACTION98
2.1417-2.19530.19452150.16945620X-RAY DIFFRACTION98
2.1953-2.25460.21311160.19092225X-RAY DIFFRACTION72
2.2546-2.3210.20041400.17723764X-RAY DIFFRACTION85
2.321-2.39590.20632300.16775687X-RAY DIFFRACTION98
2.3959-2.48150.2152250.16885743X-RAY DIFFRACTION99
2.4815-2.58090.19612320.17215747X-RAY DIFFRACTION99
2.5809-2.69840.20352460.1795741X-RAY DIFFRACTION99
2.6984-2.84060.2162540.18695761X-RAY DIFFRACTION99
2.8406-3.01860.20882670.18625771X-RAY DIFFRACTION99
3.0186-3.25170.20282960.18085756X-RAY DIFFRACTION100
3.2517-3.57890.17632970.1665789X-RAY DIFFRACTION100
3.5789-4.09670.18072890.16185633X-RAY DIFFRACTION97
4.0967-5.16120.18293080.15035875X-RAY DIFFRACTION100
5.1612-71.12780.20693110.20436013X-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)
12.1440.4492-0.28382.04570.49332.4275-0.13520.2742-0.5743-0.34390.0141-0.32010.40440.01150.10590.59240.10130.13080.3386-0.03890.446118.794-64.102724.3908
21.10150.5083-0.28541.86050.5691.4237-0.1540.2244-0.0856-0.27190.1396-0.01850.31260.22630.01990.40780.09090.07980.35510.02890.2585119.2594-50.232523.8579
30.8818-1.10210.10293.2277-0.69391.1292-0.0623-0.18490.03070.33950.10270.3391-0.1467-0.0392-0.03070.4022-0.02240.04250.2662-0.03690.2911104.6819-25.497352.0258
40.8330.2344-0.58141.45810.08482.72880.0642-0.30050.09440.1123-0.0515-0.4448-0.34470.90230.00860.2879-0.0763-0.00430.6012-0.0190.3254129.6917-29.486537.2147
51.7593-0.2510.29221.58850.56591.30860.05370.039-0.1261-0.05940.0045-0.09940.12150.1073-0.03560.09640.0354-0.01230.0885-0.01930.1002137.7828-47.772-9.3601
60.57890.4276-0.04171.4097-0.71871.1698-0.09410.18690.1401-0.35320.22030.1534-0.0777-0.1011-0.12070.23530.01320.00870.1596-0.00770.163122.4959-20.4154-30.5555
71.2643-0.0416-0.02361.13260.66521.20360.0450.1340.2517-0.14-0.06530.0893-0.2034-0.07430.02380.09310.01160.0090.11140.02820.1461118.1028-18.3025-8.6977
83.5-0.06480.34591.54550.07873.984-0.35770.10840.1729-0.56490.11150.3713-0.32640.11910.21490.43-0.0428-0.07140.1956-0.05770.3598108.4732-28.139740.1031
93.86380.0383-0.34083.31380.23362.2508-0.1056-0.0230.1659-0.1939-0.02580.5738-0.08490.01710.18460.2874-0.008-0.00520.20730.01960.251108.4863-31.068739.05
102.40491.243-1.32321.1505-0.58553.8142-0.05410.20980.2546-0.10670.1729-0.32610.02650.0238-0.13670.2340.02870.0550.16370.01990.2649129.6121-18.5466-27.0549
111.3449-0.5519-0.74920.7395-0.54711.72520.16170.14430.3074-0.38450.0684-0.4305-0.45080.1046-0.21120.2371-0.02620.08750.18770.01220.2388131.0841-17.3259-23.8315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:372)
2X-RAY DIFFRACTION2chain 'A' and (resseq 373:496)
3X-RAY DIFFRACTION3chain 'A' and (resseq 497:604)
4X-RAY DIFFRACTION4chain 'A' and (resseq 605:876)
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 2:12)
10X-RAY DIFFRACTION10chain 'E' and (resseq 21:29)
11X-RAY DIFFRACTION11chain 'F' and (resseq 1:12)

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