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- PDB-7owf: KlenTaq DNA polymerase in a ternary complex with primer/template ... -

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Basic information

Entry
Database: PDB / ID: 7owf
TitleKlenTaq DNA polymerase in a ternary complex with primer/template and the fluorescent nucleotide analog BFdUTP
Components
  • DNA polymerase I, thermostable
  • Primer
  • template
KeywordsTRANSFERASE / DNA Polymerase / KlenTaq / KTQ / artificial substrate
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 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 / Helix-hairpin-helix motif, class 2 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 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 / 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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-2IU / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 Å
AuthorsBetz, K. / Srivatsan, S.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases.
Authors: Ghosh, P. / Kropp, H.M. / Betz, K. / Ludmann, S. / Diederichs, K. / Marx, A. / Srivatsan, S.G.
History
DepositionJun 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I, thermostable
B: Primer
C: template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,41110
Polymers69,4783
Non-polymers9337
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-31 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.175, 110.175, 91.296
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

21A-1079-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I, thermostable / Taq polymerase 1


Mass: 60936.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain Primer


Mass: 3601.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain template


Mass: 4939.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 109 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-2IU / [[(2R,3S,5R)-5-[5-(1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / BFdUTP


Mass: 584.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2O15P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 6000, 0.1M Tris pH 8.0, 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000089622351 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000089622351 Å / Relative weight: 1
ReflectionResolution: 1.9→47.71 Å / Num. obs: 96475 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 45.7 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.45
Reflection shellResolution: 1.9→2.02 Å / Mean I/σ(I) obs: 0.46 / Num. unique obs: 15157 / CC1/2: 0.247 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
PHENIX1.19_4085refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.91→47.71 Å / SU ML: 0.355 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 4878 5.07 %
Rwork0.1953 91380 -
obs0.1977 96258 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.09 Å2
Refinement stepCycle: LAST / Resolution: 1.91→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 567 58 102 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01315071
X-RAY DIFFRACTIONf_angle_d1.30976984
X-RAY DIFFRACTIONf_chiral_restr0.0596764
X-RAY DIFFRACTIONf_plane_restr0.0131829
X-RAY DIFFRACTIONf_dihedral_angle_d16.44631986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.44081690.40912807X-RAY DIFFRACTION95.29
1.93-1.950.3521570.37783032X-RAY DIFFRACTION99.75
1.95-1.980.34551720.36723076X-RAY DIFFRACTION99.75
1.98-20.4261550.35133034X-RAY DIFFRACTION99.81
2-2.030.30991930.33033044X-RAY DIFFRACTION99.97
2.03-2.050.35041750.31162999X-RAY DIFFRACTION100
2.06-2.080.33291590.31053072X-RAY DIFFRACTION100
2.08-2.120.2961500.31253108X-RAY DIFFRACTION99.94
2.12-2.150.33851450.28273052X-RAY DIFFRACTION100
2.15-2.180.32091400.27363091X-RAY DIFFRACTION99.97
2.18-2.220.33911680.26193027X-RAY DIFFRACTION100
2.22-2.260.30351280.25863067X-RAY DIFFRACTION99.97
2.26-2.310.33221650.25933056X-RAY DIFFRACTION100
2.31-2.350.33291500.25623106X-RAY DIFFRACTION100
2.35-2.40.28511390.2463096X-RAY DIFFRACTION100
2.4-2.460.28351450.2413096X-RAY DIFFRACTION100
2.46-2.520.30751540.24672990X-RAY DIFFRACTION99.9
2.52-2.590.29331840.24793045X-RAY DIFFRACTION99.85
2.59-2.670.36371760.25783025X-RAY DIFFRACTION100
2.67-2.750.32151680.2543083X-RAY DIFFRACTION100
2.75-2.850.26181570.24273047X-RAY DIFFRACTION100
2.85-2.960.3131730.23823062X-RAY DIFFRACTION100
2.96-3.10.28741560.23163051X-RAY DIFFRACTION100
3.1-3.260.30951600.23153066X-RAY DIFFRACTION99.97
3.26-3.470.25381710.1943033X-RAY DIFFRACTION99.97
3.47-3.730.20391840.1773035X-RAY DIFFRACTION99.97
3.73-4.110.2011910.15153010X-RAY DIFFRACTION100
4.11-4.70.18491600.13483072X-RAY DIFFRACTION100
4.7-5.920.21041580.13913059X-RAY DIFFRACTION100
5.93-47.710.14791760.13463039X-RAY DIFFRACTION99.6
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)
15.189694763250.0127544992171-0.3488968845872.17708291299-0.007089860740633.02205535663-0.18683916972-0.0274582123388-1.23585927124-0.2227422812480.0654480532345-0.5845864658440.5325437319930.1269878769580.09296366818420.509651371219-0.1051745198680.1562760323840.443532518705-0.03970043666290.87017873384142.4511838534-42.9505226887-17.5010544362
22.29178736380.952055125783-0.7913194353382.17362622353-0.02045525639353.755951217710.0844799060254-0.03274917358830.1469640785020.113094633381-0.01374486199550.0301173192385-0.743502007884-0.228936246139-0.04822504600890.3684471867430.04773610246630.02667944600030.2943796763070.05743052933140.32214823244634.693131603-15.0493571011-2.50269427148
30.8737485838890.646211334079-0.2217097767912.48479958797-0.9919167150843.13241533831-0.14228007103-0.09269544624370.5873894211540.4293223011890.3925609189330.561743547593-1.30694668835-1.63786742476-0.1664077383340.8273494542810.4046394846020.02665983730511.417984451090.1763789048240.58480211011710.1422247653-14.098140554-6.68562230464
42.740278081640.813825286205-0.23314756241.76912611834-0.29374948393.52626256256-0.272082417540.278256853645-0.106043337569-0.323927108210.367181355810.102090036744-0.114198931041-1.1287089027-0.1058948142130.378180296072-0.03174975363360.005224717436620.7278695039070.05268199886690.32145502265319.2952498278-26.0993093997-15.4011657517
56.3567217932.662843838520.3223095692362.67783785808-1.21273414554.653515466150.114228810450.624872933353-0.986710182645-0.0959668581526-0.491346068135-0.480179612792-0.1662717636360.7009257929890.2896328158570.3614819705830.04043819531910.03511799299930.4914432594910.05394366085720.39987638053638.2684250941-23.78304471955.26351693693
65.11617287576-0.9281712638521.50783135563.115248679953.555598501716.58123156185-0.343119564418-0.6251951082610.3491032194771.59151852637-0.479729032212-0.159353695955-0.130433749611-0.6493831367110.6101382545050.8638743584950.0262252935055-0.03226505248741.095440134790.1333824105410.53935587690617.8198252012-21.50113292936.99476359163
74.091459494741.72576505757-2.55524343324.634427493370.7645644151172.83453254519-0.131173421593-0.158603498994-0.2559171663440.4000825327770.261784236863-0.5291309203590.1325140032950.528964999637-0.1601681006030.3347148107080.0420192124353-0.02207193689240.3755678427170.07181437272640.31899470808339.6123957433-24.15406753125.90095161492
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 294 through 420 )AA294 - 4202 - 128
22chain 'A' and (resid 421 through 603 )AA421 - 603129 - 311
33chain 'A' and (resid 604 through 700 )AA604 - 700312 - 408
44chain 'A' and (resid 701 through 832 )AA701 - 832409 - 540
55chain 'B' and (resid 101 through 111 )BB101 - 111
66chain 'C' and (resid 201 through 205 )CF201 - 205
77chain 'C' and (resid 206 through 216 )CF206 - 216

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