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- PDB-4f8r: Bacillus DNA Polymerase I Large Fragment complex 7 -

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Basic information

Entry
Database: PDB / ID: 4f8r
TitleBacillus DNA Polymerase I Large Fragment complex 7
Components
  • DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3')
  • DNA polymerase
KeywordsTransferase/DNA / DNA Polymerase I / 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
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.64 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: to be published
Title: Structures of a High-fidelity DNA Polymerase
Authors: Wang, W. / 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
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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*(DDG))-3')
C: DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3')
F: DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,79611
Polymers148,3156
Non-polymers4805
Water21,5101194
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3')
C: DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4466
Polymers74,1583
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-52 kcal/mol
Surface area27370 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3')
F: DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3505
Polymers74,1583
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-39 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.670, 109.370, 150.390
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: 67490.289 Da / Num. of mol.: 2 / Fragment: unp residues 287-898 / 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
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3')


Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Primer Strand / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*TP*TP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 3991.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Template Strand / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1194 / 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: 52.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 48%-54% 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: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 172238 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 29.803 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 25.19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.64-1.740.4763.9816420730352199.9
1.74-1.860.2726.96165273284261100
1.86-20.14611.958225114513157.7
2-2.20.07721.06150472257161100
2.2-2.450.04830.349197915982174.1
2.45-2.830.03638.96116082199281100
2.83-3.470.02748.9797124169501100
3.47-4.90.02457.457183913047199.7
4.9-500.02163.27391487324197.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1026refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2HVI WITH INSERTION SITE BASE PAIR, METAL IONS, AND PROTEIN RESIDUES 681-721 DELETED

2hvi


Resolution: 1.64→30.982 Å / Occupancy max: 1 / Occupancy min: 0.07 / SU ML: 0.16 / σ(F): 2.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 7474 4.52 %Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 A resolution
Rwork0.1811 ---
obs0.1821 165495 87.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.14 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: LAST / Resolution: 1.64→30.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9086 827 25 1194 11132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110321
X-RAY DIFFRACTIONf_angle_d1.38414141
X-RAY DIFFRACTIONf_chiral_restr0.0761580
X-RAY DIFFRACTIONf_plane_restr0.0071697
X-RAY DIFFRACTIONf_dihedral_angle_d15.3463986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.65860.26072680.24115102537086
1.6586-1.67820.26622730.23075187546088
1.6782-1.69860.24232760.22245235551189
1.6986-1.72010.24032830.21165382566590
1.7201-1.74270.25152820.20475357563991
1.7427-1.76660.24482910.20415538582993
1.7666-1.79190.24632910.19895529582094
1.7919-1.81860.21942940.19335570586494
1.8186-1.8470.25052940.19935601589594
1.847-1.87730.24672930.19295556584994
1.8773-1.90970.2323980.19711860195885
1.9444-1.98180.23842850.19465396568191
1.9818-2.02220.20691860.18595921610798
2.0222-2.06620.2142100.18345966617699
2.0662-2.11420.18792350.17615934616999
2.1142-2.16710.1912410.17375969621099
2.1671-2.22570.20692510.17685292554396
2.2257-2.29110.1844380.16671190122886
2.2911-2.36510.19852340.1715966620099
2.3651-2.44960.19582410.17336007624899
2.4496-2.54760.2022490.17415995624499
2.5476-2.66350.19072550.17866035629099
2.6635-2.80380.20452590.19136009626899
2.8038-2.97940.22822820.192660106292100
2.9794-3.20920.20743020.191360526354100
3.2092-3.53170.19723120.169360246336100
3.5317-4.04180.17893100.16366023633399
4.0418-5.08860.1773210.152361276448100
5.0886-30.9870.20093200.20276188650897
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)
11.95511.16340.09582.4731.11692.84590.00860.2536-0.16770.37320.11720.17060.72520.0871-0.13120.48890.09190.00810.25060.06580.2228117.8167-56.7722.2032
20.7964-0.6509-0.47581.68250.43251.8193-0.1463-0.25860.02410.47180.09690.18410.14930.08580.04390.2996-0.03640.01630.2222-0.00320.2252109.715-29.772847.9337
31.07840.0173-0.69282.1085-0.01022.5256-0.0043-0.44740.12040.29790.0954-0.3029-0.06940.5888-0.07760.19790.0013-0.05740.4731-0.01350.1732130.1055-26.729537.7724
42.2093-0.49850.56481.92880.63231.89940.12480.0685-0.3341-0.08790.0098-0.02590.24390.1348-0.10780.12240.0194-0.01860.0881-0.01860.1413137.6886-47.8752-9.218
51.19120.7866-0.69491.3889-0.11810.1909-0.08440.33430.0778-0.37670.26420.21170.1235-0.3467-0.18870.13250.0044-0.02140.17780.00820.114118.8597-28.7735-23.9845
61.09760.96960.28783.50660.32781.2808-0.12340.10960.0301-0.30760.1584-0.21710.0422-0.1554-0.05820.3297-0.02650.0310.20940.07040.2107126.6964-7.6945-37.382
71.45310.30130.23381.2440.96272.0138-0.03910.25510.0742-0.1841-0.05740.1409-0.0729-0.07170.08430.0914-0.0019-0.00890.10390.0060.113116.6825-28.5206-18.9825
83.24871.6915-3.00422.0656-1.59514.35170.04880.5860.7007-0.19240.085-0.0247-0.4326-0.3696-0.16440.2430.03210.02590.23170.09210.35119.5879-2.1358-7.3441
91.93010.38660.58361.09660.86651.5358-0.0560.0410.2114-0.0462-0.02360.0847-0.0886-0.02620.07270.07310.0068-0.00150.06510.01240.0995119.6339-23.4079-5.1054
108.8697-1.62430.31081.9849-1.91993.3405-0.44970.04270.0689-0.12620.13480.54060.118-0.25430.31550.3065-0.0155-0.06380.1808-0.08560.3246108.8162-27.996539.8769
114.02732.5474-1.30875.0432-0.44951.9311-0.0092-0.25670.3218-0.3039-0.17540.5856-0.0917-0.03280.17570.2320.0208-0.04160.24940.01110.2174109.3755-27.976837.7627
125.67610.9959-3.53021.2166-0.17414.01570.12470.56690.8875-0.28110.1871-0.37010.0369-0.0394-0.26840.23910.04610.06070.17230.08560.442129.5744-18.4493-26.6957
131.3111-0.9674-0.94421.6076-0.78912.71750.2140.21920.476-0.3004-0.0338-0.6063-0.4741-0.007-0.16740.2401-0.02830.0990.2080.03560.3025131.3143-17.2818-24.1218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 298:467)A298 - 467
2X-RAY DIFFRACTION2chain 'A' and (resseq 468:604)A468 - 604
3X-RAY DIFFRACTION3chain 'A' and (resseq 605:876)A605 - 876
4X-RAY DIFFRACTION4chain 'D' and (resseq 298:467)D298 - 467
5X-RAY DIFFRACTION5chain 'D' and (resseq 468:522)D468 - 522
6X-RAY DIFFRACTION6chain 'D' and (resseq 523:586)D523 - 586
7X-RAY DIFFRACTION7chain 'D' and (resseq 587:666)D587 - 666
8X-RAY DIFFRACTION8chain 'D' and (resseq 667:743)D667 - 743
9X-RAY DIFFRACTION9chain 'D' and (resseq 744:876)D744 - 876
10X-RAY DIFFRACTION10chain 'B' and (resseq 21:29)B21 - 101
11X-RAY DIFFRACTION11chain 'C' and (resseq 2:12)C2 - 12
12X-RAY DIFFRACTION12chain 'E' and (resseq 21:29)E21 - 101
13X-RAY DIFFRACTION13chain 'F' and (resseq 1:12)F1 - 12

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