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- PDB-6fbe: KlenTaq DNA polymerase processing a modified primer - bearing the... -

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Basic information

Entry
Database: PDB / ID: 6fbe
TitleKlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the third primer nucleotide.
Components
  • DNA (5'-D(*AP*AP*AP*CP*GP*GP*GP*TP*GP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*CP*AP*(OH3)P*CP*C)-3')
  • DNA polymerase I, thermostable
KeywordsDNA BINDING PROTEIN / DNA polymerase / modified nucleotides / KlenTaq / KlenTaq DNA polymerase
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 ...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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / 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 / 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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-XG4 / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.589 Å
AuthorsKropp, H.M. / Diederichs, K. / Marx, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Authors: Kropp, H.M. / Durr, S.L. / Peter, C. / Diederichs, K. / Marx, A.
History
DepositionDec 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Aug 14, 2019Group: Data collection / Structure summary / Category: entity / reflns / reflns_shell
Item: _entity.formula_weight / _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all

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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: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*CP*AP*(OH3)P*CP*C)-3')
C: DNA (5'-D(*AP*AP*AP*CP*GP*GP*GP*TP*GP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5139
Polymers69,7493
Non-polymers7656
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-21 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.480, 108.480, 90.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1301-

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: 61068.160 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 DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*CP*AP*(OH3)P*CP*C)-3')


Mass: 3701.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*CP*GP*GP*GP*TP*GP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4979.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 469 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 20 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.589→46.973 Å / Num. obs: 159958 / % possible obs: 99.8 % / Redundancy: 4.79 % / Rrim(I) all: 0.108 / Net I/σ(I): 8.39
Reflection shellResolution: 1.589→1.597 Å / Redundancy: 4.45 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 25710 / Rrim(I) all: 1.404 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.589→46.973 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 7935 4.96 %
Rwork0.1751 --
obs0.1766 159948 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.589→46.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 578 42 463 5308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065095
X-RAY DIFFRACTIONf_angle_d0.7047016
X-RAY DIFFRACTIONf_dihedral_angle_d15.5162993
X-RAY DIFFRACTIONf_chiral_restr0.043776
X-RAY DIFFRACTIONf_plane_restr0.004852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5888-1.60690.34852090.35554960X-RAY DIFFRACTION97
1.6069-1.62580.30512470.34175099X-RAY DIFFRACTION100
1.6258-1.64560.36582420.33535112X-RAY DIFFRACTION100
1.6456-1.66650.33182290.32195089X-RAY DIFFRACTION100
1.6665-1.68840.32372470.30885075X-RAY DIFFRACTION100
1.6884-1.71150.29232770.29085040X-RAY DIFFRACTION100
1.7115-1.7360.30982670.28425076X-RAY DIFFRACTION100
1.736-1.76190.30682720.2775107X-RAY DIFFRACTION100
1.7619-1.78940.28282600.26435048X-RAY DIFFRACTION100
1.7894-1.81880.30412680.2585045X-RAY DIFFRACTION100
1.8188-1.85010.31422860.23855085X-RAY DIFFRACTION100
1.8501-1.88380.23942610.21925107X-RAY DIFFRACTION100
1.8838-1.920.24542860.21525027X-RAY DIFFRACTION100
1.92-1.95920.24672770.20885114X-RAY DIFFRACTION100
1.9592-2.00180.22652950.20364948X-RAY DIFFRACTION100
2.0018-2.04830.23772730.20515185X-RAY DIFFRACTION100
2.0483-2.09960.21942550.18545006X-RAY DIFFRACTION100
2.0996-2.15630.21312440.16675123X-RAY DIFFRACTION100
2.1563-2.21980.19172370.1715106X-RAY DIFFRACTION100
2.2198-2.29140.20162630.16145050X-RAY DIFFRACTION100
2.2914-2.37330.2032350.15745109X-RAY DIFFRACTION100
2.3733-2.46840.18742520.16425103X-RAY DIFFRACTION100
2.4684-2.58070.20462820.16365067X-RAY DIFFRACTION100
2.5807-2.71670.20242930.16915054X-RAY DIFFRACTION100
2.7167-2.88690.21212720.16955032X-RAY DIFFRACTION100
2.8869-3.10980.21192570.1645093X-RAY DIFFRACTION100
3.1098-3.42260.16892910.15675032X-RAY DIFFRACTION100
3.4226-3.91770.16523030.14075048X-RAY DIFFRACTION100
3.9177-4.9350.15582600.12275029X-RAY DIFFRACTION99
4.935-46.99370.17952950.15975044X-RAY DIFFRACTION100
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)
10.6346-0.14450.05361.87070.0730.9420.0164-0.0269-0.2302-0.1994-0.0034-0.2390.2831-0.0022-0.01180.2679-0.04140.03110.16090.00320.272839.5778-40.8065-18.1129
20.78450.6324-0.24721.3661-0.13331.4970.1043-0.15740.08060.1938-0.08780.0903-0.2703-0.0346-0.01570.2101-0.02190.01480.1681-0.00720.216835.8526-10.63591.6645
31.11370.1123-0.1871.16-0.7032.3361-0.0123-0.22450.21420.27020.27020.2879-0.7388-1.0079-0.12020.37690.23960.03370.64450.0360.28511.552-14.1816-8.5016
41.22290.1923-0.0011.0643-0.59452.8306-0.0521-0.1317-0.0296-0.04010.18520.17550.0004-0.7216-0.1090.1266-0.0056-0.00610.32030.03620.201117.388-25.2125-13.4568
52.51991.49960.93980.95290.18183.02090.092-0.0428-0.43770.1541-0.18-0.19640.09030.31160.00890.17210.01450.04280.17840.03610.226736.4077-22.40734.2964
68.40242.675-1.05024.0364-0.45570.1362-0.0008-1.73310.72511.65760.12550.0506-0.2027-0.0273-0.17230.60260.09520.00230.8045-0.02550.281717.3085-21.17487.2558
70.9792-1.45960.61953.18621.00756.58550.0229-0.05640.00690.19050.1328-0.2075-0.25930.0845-0.1430.1401-0.03550.01650.13080.01210.152332.1387-23.317-1.8969
89.3032-6.71870.05784.88340.10270.7189-0.5937-0.3592-0.58120.84540.7376-0.0199-0.10250.5838-0.10120.28250.0406-0.03560.3852-0.01620.33145.0423-24.135512.6347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 294 through 452 )
2X-RAY DIFFRACTION2chain 'A' and (resid 453 through 603 )
3X-RAY DIFFRACTION3chain 'A' and (resid 604 through 685 )
4X-RAY DIFFRACTION4chain 'A' and (resid 686 through 832 )
5X-RAY DIFFRACTION5chain 'B' and (resid 101 through 112 )
6X-RAY DIFFRACTION6chain 'C' and (resid 201 through 205 )
7X-RAY DIFFRACTION7chain 'C' and (resid 206 through 210 )
8X-RAY DIFFRACTION8chain 'C' and (resid 211 through 216 )

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