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- PDB-4f4k: DNA Polymerase I Large Fragment Complex 6 -

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Basic information

Entry
Database: PDB / ID: 4f4k
TitleDNA Polymerase I Large Fragment Complex 6
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 / 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'-DIDEOXYGUANOSINE-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: 1.6 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 10, 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 / pdbx_struct_conn_angle / 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_alt_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_alt_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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*(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)149,26812
Polymers148,3156
Non-polymers9526
Water25,8701436
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)74,2544
Polymers74,1583
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-30 kcal/mol
Surface area27420 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)75,0148
Polymers74,1583
Non-polymers8565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-53 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.810, 109.220, 150.580
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: 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 / 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)

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Non-polymers , 5 types, 1442 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1436 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 53% 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: 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: 1.6→50 Å / Num. obs: 187320 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 27.797 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.690.5043.61170828304611100
1.69-1.810.2776.4418304131868199.9
1.81-1.950.1779.379758417867163.9
1.95-2.140.08518.2215711027190199.9
2.14-2.390.05525.7310457118583177.6
2.39-2.760.04133.5812395421442199.9
2.76-3.380.03341.0110352418117199.7
3.38-4.780.0346.967719913999198.3
4.78-500.02752.85425247793196.6

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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

2hvi


Resolution: 1.6→30.062 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.15 / σ(F): 2.35 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 8168 4.55 %Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 resolution
Rwork0.1709 ---
obs0.1719 179455 88.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.12 Å2 / Biso min: 5.72 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9294 828 54 1436 11612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110540
X-RAY DIFFRACTIONf_angle_d1.35314452
X-RAY DIFFRACTIONf_chiral_restr0.0761619
X-RAY DIFFRACTIONf_plane_restr0.0071730
X-RAY DIFFRACTIONf_dihedral_angle_d15.394101
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 (%)
1.6-1.61820.26762890.23465483577286
1.6182-1.63720.262940.2255582587688
1.6372-1.65720.24463000.21395697599789
1.6572-1.67820.25533040.21195788609290
1.6782-1.70020.23463030.20075748605191
1.7002-1.72350.23833120.19425938625092
1.7235-1.74810.2313130.18875938625193
1.7481-1.77420.23143150.18745986630193
1.7742-1.8020.21413170.18016017633494
1.802-1.83150.21783170.17916035635295
1.8315-1.86310.20773200.17576070639095
1.8631-1.89690.20972580.17584910516887
1.9334-1.97290.23792210.17624196441786
1.9729-2.01580.18782320.17086297652997
2.0158-2.06270.18222260.16216434666098
2.0627-2.11420.16952450.15796398664399
2.1142-2.17140.18122580.15866390664899
2.1714-2.23520.1692440.15925096534093
2.2352-2.30740.1864840.15812510259488
2.3074-2.38980.18262630.15896457672099
2.3898-2.48540.19352580.16296468672699
2.4854-2.59850.20052690.16466453672299
2.5985-2.73540.20342790.1726481676099
2.7354-2.90670.20812920.17696471676399
2.9067-3.13090.19083110.17876491680299
3.1309-3.44550.17883370.16576456679399
3.4455-3.94320.17483260.15656386671297
3.9432-4.96430.16993390.14566515685499
4.9643-30.06750.19953420.19716596693897
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)
11.72971.07940.28772.06040.18341.72630.04670.2771-0.4340.12730.0898-0.11360.52080.2058-0.13980.45780.1190.02470.2522-0.02960.2504119.8704-59.792725.3716
24.1722.1304-1.06273.2908-0.50931.4402-0.15670.70320.1336-0.32030.24640.28550.14950.0053-0.10440.32520.0481-0.02230.34030.01850.1543113.6922-52.047516.9618
30.7702-0.35860.14391.344-0.19161.949-0.1192-0.22240.02040.32350.1098-0.02520.25210.46850.00560.1989-0.0492-0.030.14940.00860.1488117.549-38.616646.5338
40.7813-0.9999-0.14012.185-0.14250.9175-0.0499-0.06750.00510.02940.07020.14150.0235-0.004-0.00460.2468-0.0439-0.00680.1395-0.00770.164104.7292-23.931649.1826
51.1066-0.0382-0.17651.35480.44351.3434-0.0383-0.1770.12570.32110.078-0.2504-0.03530.80560.00370.2567-0.0503-0.0590.40610.01460.1757128.0116-32.9642.3088
61.3111-0.8033-1.03542.50060.2131.32220.0132-0.38910.37850.15760.2784-0.4756-0.44870.5734-0.2620.3809-0.14360.00430.446-0.07880.3109128.7731-14.337732.5998
70.72960.7116-0.33341.14720.13042.6338-0.0955-0.1755-0.05310.2835-0.0452-0.5059-0.01061.02770.12290.23510.0266-0.06630.6290.03660.2383133.7937-36.535740.5182
81.6078-0.26530.26071.67320.50231.42370.04410.0503-0.1711-0.07440.0098-0.08230.16950.1528-0.04330.09930.0352-0.01170.0884-0.01420.0875137.9593-47.8155-9.4004
90.44450.298-0.03631.4497-0.60980.8892-0.06750.17420.09-0.3810.15970.1112-0.0055-0.0577-0.09270.18030.00310.00520.1410.00130.1245122.5716-20.2746-30.9265
100.9072-0.0829-0.08511.16280.70711.2260.0310.0910.2228-0.1171-0.06540.0996-0.1871-0.08430.02980.07390.0086-0.00170.09170.01580.1298118.1781-18.3224-8.7915
114.2912-0.5163-0.24171.4787-0.89181.3324-0.30060.15090.1022-0.34060.21510.3797-0.026-0.0980.14450.3323-0.0432-0.0740.1688-0.0330.2615108.8787-28.07640.048
122.93841.3995-0.81542.9080.01671.8177-0.02680.01160.442-0.4285-0.11260.3192-0.35770.07230.17720.27840.0048-0.05950.18810.02390.1893109.6167-28.060537.93
133.35761.3438-2.05491.2949-0.36654.0603-0.09490.30840.2146-0.19990.1189-0.42710.13570.1174-0.06820.160.03680.04030.11710.03520.2659129.739-18.4855-26.9751
141.0328-0.7023-0.49110.938-0.57681.99130.09320.16330.2545-0.29840.0723-0.3116-0.34010.2681-0.13240.1711-0.04720.06940.16340.01290.1894131.3613-17.3644-24.0291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 298:409)A298 - 409
2X-RAY DIFFRACTION2chain 'A' and (resseq 410:467)A410 - 467
3X-RAY DIFFRACTION3chain 'A' and (resseq 468:522)A468 - 522
4X-RAY DIFFRACTION4chain 'A' and (resseq 523:604)A523 - 604
5X-RAY DIFFRACTION5chain 'A' and (resseq 605:676)A605 - 676
6X-RAY DIFFRACTION6chain 'A' and (resseq 677:780)A677 - 780
7X-RAY DIFFRACTION7chain 'A' and (resseq 781:876)A781 - 876
8X-RAY DIFFRACTION8chain 'D' and (resseq 298:467)D298 - 467
9X-RAY DIFFRACTION9chain 'D' and (resseq 468:604)D468 - 604
10X-RAY DIFFRACTION10chain 'D' and (resseq 605:876)D605 - 876
11X-RAY DIFFRACTION11chain 'B' and (resseq 21:29)B21 - 101
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:12)C2 - 12
13X-RAY DIFFRACTION13chain 'E' and (resseq 21:29)E21 - 101
14X-RAY DIFFRACTION14chain 'F' and (resseq 1:12)F1 - 12

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