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

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Basic information

Entry
Database: PDB / ID: 9fmf
TitleKlenTaq DNA polymerase in a ternary complex with primer/template and a fluorobenzofuran-modified dUTP (FBFdUTP)
Components
  • DNA polymerase I, thermostable
  • DNA template
  • Primer
KeywordsTRANSFERASE / DNA Polymerase / Fluorobenzofuran / 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
: / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 6, 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
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1966
Polymers69,4783
Non-polymers7193
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-8 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.040, 110.040, 91.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
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
Details: first two N-terminal residues are not resolved / 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 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, 40 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A1IDW / [[(2~{R},3~{S},5~{R})-5-[5-(5-fluoranyl-1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 602.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18FN2O15P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Nextal Nucleix Suite condition D12: 0.2 M Ammonium chloride, 0.01 M Calcium chloride, 0.05 M TRIS HCl pH 8.5, 20% (w/v) PEG 4000

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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: 0.97623 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.1→45.664 Å / Num. obs: 545067 / % possible obs: 95.7 % / Redundancy: 7.87 % / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 11717 / CC1/2: 0.25 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_5340: ???)refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.14 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 3547 5.28 %
Rwork0.1869 --
obs0.1894 67175 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 567 45 37 4940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085062
X-RAY DIFFRACTIONf_angle_d0.9946976
X-RAY DIFFRACTIONf_dihedral_angle_d17.4431993
X-RAY DIFFRACTIONf_chiral_restr0.052765
X-RAY DIFFRACTIONf_plane_restr0.009817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.39411820.40412719X-RAY DIFFRACTION100
2.13-2.160.39481540.38742762X-RAY DIFFRACTION100
2.16-2.190.3991160.36122743X-RAY DIFFRACTION100
2.19-2.220.36721300.38422436X-RAY DIFFRACTION100
2.28-2.30.47451140.38321590X-RAY DIFFRACTION99
2.3-2.340.29221720.33742745X-RAY DIFFRACTION100
2.34-2.390.35661410.33852727X-RAY DIFFRACTION100
2.39-2.440.29271140.31242731X-RAY DIFFRACTION100
2.44-2.490.31251740.28462727X-RAY DIFFRACTION100
2.49-2.550.3381720.27712745X-RAY DIFFRACTION100
2.55-2.610.38881270.28772761X-RAY DIFFRACTION100
2.61-2.680.36371440.28562776X-RAY DIFFRACTION100
2.68-2.760.30361660.27492705X-RAY DIFFRACTION100
2.76-2.850.2651460.29082722X-RAY DIFFRACTION100
2.85-2.950.37751660.29812717X-RAY DIFFRACTION100
2.95-3.070.3171740.24542734X-RAY DIFFRACTION100
3.07-3.210.27421180.23042760X-RAY DIFFRACTION100
3.21-3.380.27521580.21622723X-RAY DIFFRACTION100
3.38-3.590.21261610.18492753X-RAY DIFFRACTION100
3.59-3.860.22811240.16622072X-RAY DIFFRACTION76
3.86-4.250.17921640.14422742X-RAY DIFFRACTION100
4.25-4.860.20341400.13492734X-RAY DIFFRACTION100
4.87-6.120.19591700.14342739X-RAY DIFFRACTION100
6.13-35.140.14321200.1182765X-RAY DIFFRACTION99
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)
10.87910.3810.56040.41660.18030.56980.2040.04150.04550.1205-0.1472-0.5634-0.07810.228900.71710.04620.08240.55960.1020.964158.535415.2323-2.3342
20.5651-0.55340.09011.9297-0.34471.41030.02660.03970.0353-0.02470.0652-0.0502-0.1079-0.545600.49930.051-0.00310.59820.050.562530.508322.500912.7026
31.3594-0.07560.58290.58570.08542.3730.226-0.1535-0.0232-0.2515-0.1031-0.11530.6463-0.9768-0.00020.7608-0.2181-0.06920.8080.04120.516726.00952.77723.5307
40.0413-0.1044-0.02440.1118-0.17710.4425-0.50460.13930.1562-0.21710.3056-0.3406-0.5791-0.22570.00020.6888-0.1123-0.10070.6440.01720.718739.691621.353220.5129
50.0682-0.0234-0.05150.05620.04570.0196-0.4455-0.56330.42660.0638-0.2781-0.03170.0935-0.64330.00041.0067-0.3383-0.12480.9415-0.06130.618127.54494.572822.3486
60.1178-0.0565-0.02030.0315-0.0016-0.0050.4006-0.29830.00240.1102-0.442-0.02620.2654-0.28680.00070.7251-0.1143-0.01770.59030.0370.639236.805716.207313.2019
70.3501-0.0480.1880.0037-0.08030.15070.0723-0.82440.4911-0.35690.1763-0.6766-1.20850.47140.04420.6345-0.1644-0.06970.9008-0.09320.838343.981427.282427.5556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 295 through 420 )
2X-RAY DIFFRACTION2chain 'A' and (resid 421 through 603 )
3X-RAY DIFFRACTION3chain 'A' and (resid 604 through 832 )
4X-RAY DIFFRACTION4chain 'B' and (resid 101 through 111 )
5X-RAY DIFFRACTION5chain 'C' and (resid 201 through 205 )
6X-RAY DIFFRACTION6chain 'C' and (resid 206 through 210 )
7X-RAY DIFFRACTION7chain 'C' and (resid 211 through 216 )

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