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- PDB-4ez9: Bacillus DNA Polymerase I Large Fragment Complex 2 -

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Basic information

Entry
Database: PDB / ID: 4ez9
TitleBacillus DNA Polymerase I Large Fragment Complex 2
Components
  • DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
  • DNA polymerase
KeywordsTransferase/DNA / DNA Polymerase I / protein-DNA complex / closed form / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 ...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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 3'-5' exonuclease domain / 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'-DIDEOXY-THYMIDINE-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 1.1Feb 4, 2015Group: Other
Revision 1.2Sep 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*(2DT))-3')
C: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
F: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,09010
Polymers148,3136
Non-polymers7764
Water24,5541363
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
C: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3715
Polymers74,1573
Non-polymers2142
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-36 kcal/mol
Surface area27490 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
F: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7195
Polymers74,1573
Non-polymers5622
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-31 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.920, 108.960, 149.490
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*(2DT))-3')


Mass: 2650.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Primer Strand
#3: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4015.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Template Strand

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Non-polymers , 4 types, 1367 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-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-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1363 / 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: 52.3 %
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: ALS / Beamline: 12.3.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 171000 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 28.337 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 22.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.64-1.740.4963.85199.9
1.74-1.860.3016.25199.9
1.86-20.1819.35159.9
2-2.190.09617.5199.9
2.19-2.450.06124.54176.1
2.45-2.830.04233.96199.7
2.83-3.460.02845.53199.2
3.46-4.880.02257.21197.9
4.88-500.01868.78192.5

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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→43.125 Å / Occupancy max: 1 / Occupancy min: 0.07 / SU ML: 0.14 / σ(F): 2.35 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 7358 4.55 %
Rwork0.168 --
obs0.1691 161679 86.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→43.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9280 828 46 1363 11517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110478
X-RAY DIFFRACTIONf_angle_d1.34814360
X-RAY DIFFRACTIONf_dihedral_angle_d15.3274058
X-RAY DIFFRACTIONf_chiral_restr0.0771613
X-RAY DIFFRACTIONf_plane_restr0.0071716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65860.23292690.21385124X-RAY DIFFRACTION86
1.6586-1.67820.25912710.21015144X-RAY DIFFRACTION88
1.6782-1.69860.2442740.20315200X-RAY DIFFRACTION89
1.6986-1.72010.25022770.19925270X-RAY DIFFRACTION90
1.7201-1.74280.2352820.18975349X-RAY DIFFRACTION91
1.7428-1.76660.21062790.18295300X-RAY DIFFRACTION91
1.7666-1.79190.22062840.1785394X-RAY DIFFRACTION92
1.7919-1.81860.2162860.17615449X-RAY DIFFRACTION92
1.8186-1.8470.20612850.17675415X-RAY DIFFRACTION92
1.847-1.87730.22332760.17275241X-RAY DIFFRACTION89
1.8773-1.90970.23011150.1782181X-RAY DIFFRACTION77
1.9097-1.94440.103510.13398X-RAY DIFFRACTION19
1.9444-1.98180.22262630.18125003X-RAY DIFFRACTION85
1.9818-2.02230.19022190.17055762X-RAY DIFFRACTION96
2.0223-2.06620.18432110.16385796X-RAY DIFFRACTION97
2.0662-2.11430.18772330.16235854X-RAY DIFFRACTION98
2.1143-2.16720.18812280.16185829X-RAY DIFFRACTION98
2.1672-2.22580.21042620.16885270X-RAY DIFFRACTION89
2.2258-2.29130.2276390.17371107X-RAY DIFFRACTION81
2.2913-2.36520.18332240.15655775X-RAY DIFFRACTION96
2.3652-2.44970.19352340.15735877X-RAY DIFFRACTION98
2.4497-2.54780.16832450.15725886X-RAY DIFFRACTION98
2.5478-2.66370.17322510.16335896X-RAY DIFFRACTION98
2.6637-2.80420.18352560.17075880X-RAY DIFFRACTION98
2.8042-2.97980.19782780.16985873X-RAY DIFFRACTION98
2.9798-3.20980.19062920.17215943X-RAY DIFFRACTION99
3.2098-3.53270.17313120.16115875X-RAY DIFFRACTION98
3.5327-4.04360.18662990.16455855X-RAY DIFFRACTION97
4.0436-5.09320.16273090.1395944X-RAY DIFFRACTION98
5.0932-43.14020.19643040.19615821X-RAY DIFFRACTION92
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)
11.39880.6739-0.19812.3232-0.15321.4717-0.14160.2101-0.3923-0.41920.0706-0.25080.36110.05160.07960.4090.05370.10680.2248-0.02010.2782119.9829-59.560225.4924
20.711-0.331-0.28441.46690.24241.4911-0.0447-0.00530.0035-0.00820.0019-0.0175-0.01970.21740.05220.1704-0.0474-0.02050.16880.02460.1269115.7149-35.344939.9055
35.38720.1957-0.04722.76370.33552.3732-0.212-1.54910.44260.01290.3421-0.7467-1.08450.4324-0.11860.62090.02110.00330.7159-0.17850.5099129.8458-9.368140.2717
40.9350.3875-0.65971.1785-0.07432.71710.004-0.18530.0333-0.0247-0.1042-0.4265-0.10970.8690.09850.1832-0.04970.01380.45310.00530.2544132.0972-32.572934.6155
50.408-0.06490.11280.9722-0.19290.69670.01840.0655-0.0001-0.15490.0179-0.04130.02620.0495-0.0370.0923-0.00380.01680.1035-0.02950.0909131.2374-35.2537-19.0391
60.93360.0238-0.10621.11480.47681.10060.04840.11390.1541-0.0817-0.04910.0889-0.1228-0.08870.00220.06530.01770.0080.11340.02020.1243118.4814-18.0668-8.5447
74.1885-0.5219-0.26070.9643-0.05942.6795-0.16370.0313-0.113-0.55660.08240.2612-0.1172-0.14620.09250.3086-0.0662-0.07630.1259-0.02610.2121108.8756-28.014440.0605
82.26560.2311-0.54682.24350.10132.06970.09130.08770.2832-0.2753-0.06290.3753-0.3321-0.0108-0.00280.22310.0028-0.03010.15580.01250.1821109.9828-27.952437.8676
92.30030.8812-0.83690.8458-0.92494.3319-0.04770.3019-0.0198-0.06020.0666-0.34330.05610.0203-0.05860.16250.02410.03720.1058-0.01870.2315129.9347-18.5852-26.9085
100.6608-0.4925-0.27140.8594-0.04071.79350.1060.16510.1443-0.42250.1413-0.3992-0.27010.2394-0.21330.1656-0.02940.09320.1671-00.1803131.4037-17.4703-23.8326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 298:409)
2X-RAY DIFFRACTION2chain 'A' and (resseq 410:676)
3X-RAY DIFFRACTION3chain 'A' and (resseq 677:743)
4X-RAY DIFFRACTION4chain 'A' and (resseq 744:875)
5X-RAY DIFFRACTION5chain 'D' and (resseq 298:604)
6X-RAY DIFFRACTION6chain 'D' and (resseq 605:876)
7X-RAY DIFFRACTION7chain 'B' and (resseq 21:29)
8X-RAY DIFFRACTION8chain 'C' and (resseq 2:12)
9X-RAY DIFFRACTION9chain 'E' and (resseq 21:29)
10X-RAY DIFFRACTION10chain 'F' and (resseq 1:12)

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