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- PDB-4ez6: Bacillus DNA Polymerase I Large Fragment Complex 1 -

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Basic information

Entry
Database: PDB / ID: 4ez6
TitleBacillus DNA Polymerase I Large Fragment Complex 1
Components
  • DNA (5'-D(*CP*AP*TP*GP*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 / protein-DNA complex / closed form / Transferase-DNA complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / 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'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
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 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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*GP*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*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,56210
Polymers148,3656
Non-polymers1,1974
Water24,5721364
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*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7925
Polymers74,1833
Non-polymers6092
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-25 kcal/mol
Surface area26820 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*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7705
Polymers74,1833
Non-polymers5872
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-26 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.740, 109.510, 149.800
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: Bacillus Fragment (analogous to E. coli Klenow Fragment, unp residues 287-878)
Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / 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*(DDG))-3')


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


Mass: 4016.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Template Strand

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Non-polymers , 4 types, 1368 molecules

#4: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1364 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 48%-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: 0.97121 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 166080 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 26.512 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.63
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.64-1.740.4573.63198.3
1.74-1.850.2835.67198.5
1.85-20.1858.04160.1
2-2.190.10314197.7
2.19-2.450.0719.22173.2
2.45-2.830.05224.81196
2.83-3.460.03831.56194.5
3.46-4.880.03337.08190.6
4.88-500.02546.53186.6

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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→46.87 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.14 / σ(F): 2.35 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 7159 4.52 %
Rwork0.1708 --
obs0.1717 158215 83.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9046 832 73 1364 11315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110279
X-RAY DIFFRACTIONf_angle_d1.35514096
X-RAY DIFFRACTIONf_dihedral_angle_d15.5793993
X-RAY DIFFRACTIONf_chiral_restr0.0761576
X-RAY DIFFRACTIONf_plane_restr0.0071675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65860.24752710.22435152X-RAY DIFFRACTION87
1.6586-1.67820.26392680.21065095X-RAY DIFFRACTION87
1.6782-1.69860.22792750.20525213X-RAY DIFFRACTION89
1.6986-1.72010.20892760.19245248X-RAY DIFFRACTION89
1.7201-1.74280.21082780.19455297X-RAY DIFFRACTION89
1.7428-1.76660.21852820.18495354X-RAY DIFFRACTION90
1.7666-1.79190.22862830.18215379X-RAY DIFFRACTION91
1.7919-1.81860.23872860.17685419X-RAY DIFFRACTION92
1.8186-1.8470.21042840.1785394X-RAY DIFFRACTION91
1.847-1.87730.23362820.17575369X-RAY DIFFRACTION90
1.8773-1.90970.2218960.16971810X-RAY DIFFRACTION71
1.9097-1.94440.127210.227727X-RAY DIFFRACTION13
1.9444-1.98180.20572670.17645048X-RAY DIFFRACTION85
1.9818-2.02230.20071880.16965708X-RAY DIFFRACTION95
2.0223-2.06630.17662020.16045756X-RAY DIFFRACTION95
2.0663-2.11430.18732300.16095694X-RAY DIFFRACTION95
2.1143-2.16720.16672260.1565796X-RAY DIFFRACTION96
2.1672-2.22580.18482310.15725044X-RAY DIFFRACTION88
2.2258-2.29130.1592430.1591108X-RAY DIFFRACTION73
2.2913-2.36520.19322210.1575709X-RAY DIFFRACTION95
2.3652-2.44980.17832310.15785786X-RAY DIFFRACTION96
2.4498-2.54780.17672470.15965740X-RAY DIFFRACTION95
2.5478-2.66380.18572420.16555765X-RAY DIFFRACTION95
2.6638-2.80420.17822470.17265705X-RAY DIFFRACTION95
2.8042-2.97990.18942640.17695695X-RAY DIFFRACTION95
2.9799-3.20990.20522830.17595704X-RAY DIFFRACTION94
3.2099-3.53280.17242970.16295602X-RAY DIFFRACTION93
3.5328-4.04380.19122800.17345393X-RAY DIFFRACTION89
4.0438-5.09380.1552870.14535580X-RAY DIFFRACTION91
5.0938-46.88910.21332910.19965466X-RAY DIFFRACTION86
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)
11.69820.8634-0.55681.8221-0.47031.3709-0.01980.3671-0.1072-0.5801-0.005-0.11610.1678-0.0210.02320.45310.07560.09380.26760.02190.2164117.8337-57.643222.7171
20.612-0.4750.0042.3581-0.15860.7604-0.0501-0.08170.06040.1828-0.0314-0.1232-0.05210.11940.07870.206-0.0447-0.01840.16420.02260.144114.7914-31.834646.79
32.5721-0.82820.15321.11640.45952.7438-0.0348-0.21720.4529-0.5104-0.0608-0.4425-0.48610.22010.1030.5118-0.03570.1450.25670.06620.3715126.8146-16.614129.9688
40.73550.33-0.21022.0843-0.2872.37220.0016-0.1454-0.04320.0421-0.2902-1.0196-0.20970.75470.27310.2191-0.04150.04590.44180.12520.4805133.7264-37.268141.1801
51.5196-0.02390.40021.49890.44611.28980.02190.0413-0.1144-0.040.0203-0.07670.10590.0912-0.03770.08860.0275-0.00940.0933-0.01710.0736138.4835-47.8962-9.4209
60.49120.18280.02831.3003-0.43660.7835-0.0410.13130.1018-0.30150.11020.0978-0.0627-0.029-0.06370.15940.01660.01410.1213-0.01120.1147122.63-20.3225-30.563
70.90880.12070.05381.20170.67061.10760.01720.0920.1649-0.0945-0.04230.1083-0.1625-0.04670.0180.07010.01520.00550.09010.01540.096118.515-18.4036-8.6657
88.2292-1.29621.0662.7348-0.61554.3769-0.17460.01210.1354-0.69590.00370.2462-0.1162-0.23170.20040.3445-0.0416-0.04380.1094-0.01280.2149108.9532-28.263140.0525
93.66291.2684-0.98373.2441-0.14432.262-0.04290.0340.3565-0.5673-0.1230.3948-0.23340.02330.1570.28050.0062-0.06090.17010.02640.1904110.1995-28.233737.8572
102.56281.7405-1.55371.4289-0.42695.4232-0.0420.22560.0362-0.14810.1173-0.3713-0.0660.2468-0.10990.17410.03950.03790.11120.00550.2208129.7217-18.5316-26.7674
111.1291-0.7202-0.71650.6715-0.25522.70650.15640.08470.1438-0.34790.0614-0.2966-0.35550.1559-0.21630.1642-0.03010.07110.131-0.00120.1418131.3916-17.3989-23.9411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:467)
2X-RAY DIFFRACTION2chain 'A' and (resseq 468:699)
3X-RAY DIFFRACTION3chain 'A' and (resseq 700:780)
4X-RAY DIFFRACTION4chain 'A' and (resseq 781:876)
5X-RAY DIFFRACTION5chain 'D' and (resseq 297:467)
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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