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- PDB-4f3o: DNA Polymerase I Large Fragment Complex 5 -

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Basic information

Entry
Database: PDB / ID: 4f3o
TitleDNA Polymerase I Large Fragment Complex 5
Components
  • DNA (5'-D(*C*AP*TP*GP*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 / 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 / 5'-3' exonuclease, C-terminal domain superfamily / 3'-5' exonuclease / 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
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.57 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 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_close_contact / struct_conn / struct_conn_type / 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_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.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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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*(2DT))-3')
C: DNA (5'-D(*C*AP*TP*GP*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(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,44214
Polymers148,3636
Non-polymers1,0788
Water24,5901365
1
A: DNA polymerase
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
C: DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5477
Polymers74,1823
Non-polymers3654
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-50 kcal/mol
Surface area27400 Å2
MethodPISA
2
D: DNA polymerase
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')
F: DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8957
Polymers74,1823
Non-polymers7134
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-48 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.830, 109.330, 150.110
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: unp residues 287-878 / Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: GK2730, polA / 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 / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4040.647 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA Template Strand / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 1373 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1365 / 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: 52.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 49%-51% 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: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.57→100 Å / Num. obs: 199455 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 27.766 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.57-1.660.4623.7517496232723199.9
1.66-1.780.2586.94194761340491100
1.78-1.920.15211.1913524624092180.9
1.92-2.10.13822.0125762923103183.9
2.1-2.350.08730.922820820541180
2.35-2.710.05842.41256138223241100
2.71-3.320.04152.35216316192001100
3.32-4.690.03362.515796014940199.9
4.69-1000.02769.29872738483199.6

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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: 1.57→79.565 Å / Occupancy max: 1 / Occupancy min: 0.03 / SU ML: 0.15 / σ(F): 2.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 8791 4.58 %Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 resolution
Rwork0.1792 ---
obs0.1803 191796 89.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.94 Å2 / Biso min: 6.63 Å2
Refinement stepCycle: LAST / Resolution: 1.57→79.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9185 850 58 1365 11458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110418
X-RAY DIFFRACTIONf_angle_d1.35714282
X-RAY DIFFRACTIONf_chiral_restr0.0761599
X-RAY DIFFRACTIONf_plane_restr0.0071700
X-RAY DIFFRACTIONf_dihedral_angle_d15.2364040
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 (%)
1.57-1.58780.27843050.2585800610586
1.5878-1.60650.23883150.23795984629989
1.6065-1.62610.25893160.22655999631589
1.6261-1.64670.23923240.22236161648591
1.6467-1.66840.2493250.21716178650392
1.6684-1.69120.24243290.21076254658393
1.6912-1.71540.24543330.21126324665794
1.7154-1.7410.24463350.20696358669394
1.741-1.76820.21993380.20096423676195
1.7682-1.79720.21423370.18916417675495
1.7972-1.82820.22633420.18746482682496
1.8282-1.86140.22483400.1876464680496
1.8614-1.89720.21712730.18595187546083
1.936-1.97810.23192630.18345010527391
1.9781-2.02410.2132560.17796767702398
2.0241-2.07470.1752390.16916775701499
2.0747-2.13080.18822710.16886835710699
2.1308-2.19350.19622710.16886775704699
2.1935-2.26430.1911510.16732901305288
2.2643-2.34530.20162150.16775705592096
2.3453-2.43920.19262730.16926826709999
2.4392-2.55020.18482800.16816834711499
2.5502-2.68460.20532860.176668987184100
2.6846-2.85280.21953070.185168627169100
2.8528-3.07310.21983310.185868447175100
3.0731-3.38240.19773560.174568717227100
3.3824-3.87180.18663450.16469187263100
3.8718-4.8780.18063650.151369507315100
4.878-79.66730.19873700.20057203757399
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)
11.78511.0143-0.26991.9075-0.20621.2684-0.21430.3901-0.3013-0.45390.123-0.13990.34510.12460.08680.45260.06890.13850.3371-0.0040.2698117.7938-57.386822.6268
20.7994-0.6727-0.06432.23740.0361.3643-0.0899-0.08440.03160.25450.00320.0823-0.12750.14020.0830.2123-0.06280.00320.16610.01220.1513111.4563-31.149246.5685
30.47120.1097-0.54911.6318-0.31242.61540.0353-0.27230.12190.1409-0.1548-0.5687-0.55410.86580.11860.3265-0.154-0.01040.63930.05070.381131.4998-28.006537.7497
41.6462-0.1180.44311.75050.54211.4760.04310.0418-0.1244-0.04950.0076-0.08530.13670.0869-0.04280.09250.0276-0.00810.0936-0.0170.0881138.3239-47.8477-9.4905
50.52160.2534-0.08391.3515-0.54351.1285-0.06050.18160.1108-0.32140.16120.1192-0.1867-0.0603-0.10340.23870.00150.00020.1547-0.00680.1378122.6348-20.4868-30.6283
60.9797-0.1105-0.0951.1190.57211.13990.05130.11080.1985-0.1036-0.04860.0738-0.17-0.0597-0.00240.0750.00910.00960.10190.0190.1242118.3793-18.2895-8.7147
76.043-0.40210.29962.2921-0.0564.6638-0.24250.1384-0.1296-0.71130.0410.3875-0.2805-0.22070.19110.4015-0.0722-0.09620.1453-0.02250.2437108.9703-28.200940.0404
84.07910.9771-1.30443.04430.57422.0999-0.09740.24870.6534-0.40040.05160.5122-0.3119-0.03260.03640.2621-0.0318-0.0610.2120.04650.2694110.6011-27.10137.1051
94.11481.5796-1.63852.2649-0.58235.5084-0.07970.32280.0118-0.17530.0763-0.4439-0.03460.3613-0.02690.16590.02220.02270.1525-0.00210.2326129.8098-18.4697-26.8714
101.1297-0.6122-0.75380.4869-0.11262.38990.17270.1870.216-0.48140.1192-0.4299-0.38540.2051-0.2310.2139-0.02520.09930.18250.0090.1763131.3157-17.4136-23.8788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 297:467)A297 - 467
2X-RAY DIFFRACTION2chain 'A' and (resseq 468:630)A468 - 630
3X-RAY DIFFRACTION3chain 'A' and (resseq 631:875)A631 - 875
4X-RAY DIFFRACTION4chain 'D' and (resseq 298:467)D298 - 467
5X-RAY DIFFRACTION5chain 'D' and (resseq 468:604)D468 - 604
6X-RAY DIFFRACTION6chain 'D' and (resseq 605:876)D605 - 876
7X-RAY DIFFRACTION7chain 'B' and (resseq 21:29)B21 - 101
8X-RAY DIFFRACTION8chain 'C' and (resseq 1:12)C1 - 12
9X-RAY DIFFRACTION9chain 'E' and (resseq 21:29)E21 - 101
10X-RAY DIFFRACTION10chain 'F' and (resseq 1:12)F1 - 12

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