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- PDB-6fbi: KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp ... -

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Basic information

Entry
Database: PDB / ID: 6fbi
TitleKlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site
Components
  • DNA (5'-D(*AP*AP*AP*CP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*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 / 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 / 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: 1.9 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
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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

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


Theoretical massNumber of molelcules
Total (without water)70,4279
Polymers69,6253
Non-polymers8026
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-17 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.770, 109.770, 91.460
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-1150-

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*GP*CP*CP*AP*C)-3')


Mass: 3617.371 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*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


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, 215 molecules

#4: 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 44.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: (A) 16 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES (B) 17 % PEG 4000, 0.1 M ammonium acetate, 0.1 M HEPES, 20 mM manganese(II) chloride (C) 15 % PEG 4000, 0.1 M ...Details: (A) 16 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES (B) 17 % PEG 4000, 0.1 M ammonium acetate, 0.1 M HEPES, 20 mM manganese(II) chloride (C) 15 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.532 Å / Num. obs: 97132 / % possible obs: 100 % / Redundancy: 14.95 % / Rrim(I) all: 0.12 / Net I/σ(I): 14.61
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 14.58 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7175 / Rrim(I) all: 2.445 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.9→47.532 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.43
RfactorNum. reflection% reflection
Rfree0.2352 4891 5.05 %
Rwork0.2071 --
obs0.2086 96941 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 568 45 209 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044941
X-RAY DIFFRACTIONf_angle_d0.7136829
X-RAY DIFFRACTIONf_dihedral_angle_d15.9512892
X-RAY DIFFRACTIONf_chiral_restr0.043765
X-RAY DIFFRACTIONf_plane_restr0.004801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.92150.53561540.52793052X-RAY DIFFRACTION100
1.9215-1.94410.54511540.43862873X-RAY DIFFRACTION94
1.9441-1.96780.34221600.32583082X-RAY DIFFRACTION100
1.9678-1.99280.31861710.3163082X-RAY DIFFRACTION100
1.9928-2.0190.31891830.30573063X-RAY DIFFRACTION100
2.019-2.04660.36611860.29733070X-RAY DIFFRACTION100
2.0466-2.07590.30471570.30393076X-RAY DIFFRACTION100
2.0759-2.10690.27481510.27723089X-RAY DIFFRACTION100
2.1069-2.13980.34691550.27723058X-RAY DIFFRACTION100
2.1398-2.17490.28311380.25993137X-RAY DIFFRACTION100
2.1749-2.21240.28641590.2572997X-RAY DIFFRACTION100
2.2124-2.25260.33831340.30963122X-RAY DIFFRACTION100
2.2526-2.29590.29551690.28673091X-RAY DIFFRACTION100
2.2959-2.34280.28391550.2543156X-RAY DIFFRACTION100
2.3428-2.39370.26491340.23223026X-RAY DIFFRACTION100
2.3937-2.44940.26261460.2253097X-RAY DIFFRACTION100
2.4494-2.51070.25351550.2263122X-RAY DIFFRACTION100
2.5107-2.57850.29141770.24113033X-RAY DIFFRACTION100
2.5785-2.65440.32471790.23773028X-RAY DIFFRACTION100
2.6544-2.74010.28591740.24373106X-RAY DIFFRACTION100
2.7401-2.8380.25151650.23943051X-RAY DIFFRACTION100
2.838-2.95160.27751690.24353068X-RAY DIFFRACTION100
2.9516-3.08590.27191560.22763091X-RAY DIFFRACTION100
3.0859-3.24860.21921620.21543097X-RAY DIFFRACTION100
3.2486-3.45210.22321690.19583062X-RAY DIFFRACTION100
3.4521-3.71850.19431840.18363046X-RAY DIFFRACTION100
3.7185-4.09250.21461970.16423058X-RAY DIFFRACTION100
4.0925-4.68430.1811580.13723074X-RAY DIFFRACTION100
4.6843-5.89990.17681580.14873075X-RAY DIFFRACTION100
5.8999-47.54670.15751820.15423068X-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)
11.7388-0.12130.19251.31850.42921.8757-0.01290.05-0.783-0.21480.0829-0.39460.3241-0.084-0.04430.3584-0.15240.10750.3536-0.0480.63139.5384-40.6135-18.1776
21.461.0268-0.57011.4865-0.37962.59610.1683-0.10660.21590.1074-0.09370.005-1.094-0.2054-0.03560.52830.05850.03690.21610.01130.366435.6848-11.15941.6488
31.85790.49450.24511.3916-0.23262.9189-0.1051-0.11590.0522-0.23140.23210.2451-1.0198-1.6965-0.06520.34660.2088-0.01640.98220.09220.343115.6502-21.3578-11.8237
43.73221.45560.53790.7216-0.3462.45380.16220.5475-0.4593-0.1308-0.4501-0.282-0.24480.46860.14620.29430.09690.05620.34850.07160.353537.0207-23.14754.0723
52.46362.3343-0.84616.5664-2.02770.6384-0.0184-1.99030.4591.25530.1278-0.034-0.25550.03480.08930.46720.1974-0.02791.37580.02330.444117.574-21.5477.1725
61.4317-0.6525-1.43932.75190.54551.427-0.0963-0.1741-0.230.22250.2701-0.382-0.0476-0.1957-0.1660.21230.0223-0.0060.25110.08490.322539.5388-24.07695.7726
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 832 )
4X-RAY DIFFRACTION4chain 'B' and (resid 101 through 112 )
5X-RAY DIFFRACTION5chain 'C' and (resid 201 through 205 )
6X-RAY DIFFRACTION6chain 'C' and (resid 206 through 216 )

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