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- PDB-9fm3: KlenTaq DNA polymerase in a ternary complex with primer/template ... -

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Basic information

Entry
Database: PDB / ID: 9fm3
TitleKlenTaq DNA polymerase in a ternary complex with primer/template and a selenophene-modified dUTP (SedUTP)
Components
  • DNA polymerase I, thermostable
  • DNA template
  • Primer with terminal DOC
KeywordsTRANSFERASE / DNA Polymerase / Selenophene / Fluorescent nucleotide probe / KlenTaq
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / 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
: / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBetz, K. / Srivatsan, S.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes.
Authors: Ghosh, P. / Betz, K. / Gutfreund, C. / Pal, A. / Marx, A. / Srivatsan, S.G.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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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 with terminal DOC
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1176
Polymers69,2043
Non-polymers9133
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-11 kcal/mol
Surface area25250 Å2
Unit cell
Length a, b, c (Å)114.164, 114.164, 91.399
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

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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 with terminal DOC


Mass: 3328.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA 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, 14 molecules

#4: Chemical ChemComp-A1IDZ / [[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 597.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O14P3Se / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DOC / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 291.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O6P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: JBScreen Nuc-Pro HTS condition F12: 1M di-Sodium tartrate, 50 mM TRIS pH 7.5, 30 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.59→48.42 Å / Num. obs: 38932 / % possible obs: 94.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 81.12 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.171 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.59-2.7565920.4072.542199.4
2.75-2.9462890.6631.4811100
2.94-3.1758250.910.7871
3.17-3.4844180.9660.4731
3.48-3.8838750.9820.3341
3.88-4.4839030.9910.1811
4.48-5.4736430.9930.141

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→35.67 Å / SU ML: 0.4963 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.7461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 1925 4.95 %
Rwork0.1873 36986 -
obs0.1901 38911 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.67 Å2
Refinement stepCycle: LAST / Resolution: 2.59→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 34 11 4903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365051
X-RAY DIFFRACTIONf_angle_d0.56836961
X-RAY DIFFRACTIONf_chiral_restr0.0387765
X-RAY DIFFRACTIONf_plane_restr0.0055813
X-RAY DIFFRACTIONf_dihedral_angle_d15.11921986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.660.34751520.37032768X-RAY DIFFRACTION98.68
2.66-2.730.34791040.35632780X-RAY DIFFRACTION99.97
2.73-2.810.29851260.31782851X-RAY DIFFRACTION100
2.81-2.90.40551400.32452801X-RAY DIFFRACTION100
2.9-30.34581680.29462776X-RAY DIFFRACTION100
3.01-3.120.33371560.26882804X-RAY DIFFRACTION100
3.13-3.270.32171820.23352774X-RAY DIFFRACTION99.97
3.27-3.410.33481190.25762256X-RAY DIFFRACTION98.79
3.46-3.630.27191060.21972159X-RAY DIFFRACTION96.75
3.69-3.940.2888780.19741820X-RAY DIFFRACTION75.26
3.94-4.330.26441350.1782800X-RAY DIFFRACTION99.93
4.33-4.960.20191650.1592796X-RAY DIFFRACTION99.97
4.96-6.230.18761360.15572794X-RAY DIFFRACTION100
6.24-35.670.19191580.12242807X-RAY DIFFRACTION99.8
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)
10.8568653305380.901965215706-0.1088775367611.08145224898-0.8273354366271.763386818330.05100476271470.1538343547750.010896538995-0.0624554332521-0.160449534353-0.1049224465170.08953079670230.3347812037275.74220170177E-50.6299630219230.155420828308-0.00901879515610.7154156561940.06795060109790.64132832290258.587475999914.6246700462-3.03674861175
20.2371062212490.575025431945-0.2640772219250.771945467840.1320156057141.233278763230.1177558896160.008430959738590.3345109445170.136142771996-0.1209204324730.21051365099-0.122085698651-0.02840589920721.7634594797E-70.6967310044030.1629107029160.06797164339260.6345281948980.04044433812490.80470231415930.225528527425.245663361916.867763641
30.6904856680080.391404330343-0.3631724559160.601985644814-0.5388544540420.3107723892230.123098840866-0.01204438021180.293282291096-0.0351381771012-0.01592665833660.1489903098190.0807705082861-0.561646354230.000102582528580.759990842432-0.0343295686994-0.07498150193210.8290394408760.01834075322570.72288888871221.5996706712.661331028596.44051195181
40.9833379503690.428019242239-0.01477330826830.3247640671210.144263977161.164003216380.003592595486790.135836035273-0.00281372378858-0.1856594983040.02527959472670.002068800274420.43894162013-0.241166271515-1.18621984992E-60.850042663103-0.0177199601656-0.06357071839170.55921504320.04196562239050.59421756574434.06132218672.502922316861.7386121342
50.117775640749-0.2608873335990.1812300710670.215519232768-0.4722267211690.649253835691-0.34975429131-0.28605628473-0.0477348905643-0.0128031718843-0.0251599857021-0.0728140967253-0.95277091509-0.3262913305890.0005416365844170.901436391451-0.072119150696-0.09540491077670.7150738802940.02533139606060.88412652537841.62572461421.274876684819.6127170843
60.06811361096390.03217894858050.07614644787660.009174000798240.02924313289460.103354232421-0.638926269589-0.5943209370361.114724225960.6800076430460.472491228077-0.171890637719-0.176697976717-0.567054742180.0004447754154140.9149903030760.0296893244578-0.02972490236390.799490417027-0.004310527729140.75349114959731.00969704924.3947704110822.359220368
70.004294502195280.0360084086044-0.1016156492590.0292574938399-0.05775126153010.07102476273720.366448843381-1.29734231524-0.3494843958190.207759734834-0.8353299077830.928327099826-0.1578643207690.000734026753263-0.0002528918546470.7334854002970.02051293860890.06504018092870.699180438254-0.01218002314820.749130231939.935855316216.262322487513.251891092
80.170377807766-0.00700693831359-0.0332103380781-0.0298717073673-0.0385750491158-0.0124702188253-0.572793261341-0.3564236155850.411143974155-0.6055227606470.148536108590.0464734626748-2.223089797440.362359486935-8.51583975948E-51.01548140556-0.176479169289-0.1133764372510.940892845281-0.1305842731080.83760947529546.348474183528.282026911927.7583355825
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 452 )AA294 - 4522 - 160
22chain 'A' and (resid 453 through 603 )AA453 - 603161 - 311
33chain 'A' and (resid 604 through 685 )AA604 - 685312 - 393
44chain 'A' and (resid 686 through 832 )AA686 - 832394 - 540
55chain 'B' and (resid 101 through 112 )BC101 - 112
66chain 'C' and (resid 201 through 205 )CD201 - 205
77chain 'C' and (resid 206 through 210 )CD206 - 210
88chain 'C' and (resid 211 through 216 )CD211 - 216

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