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

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Basic information

Entry
Database: PDB / ID: 6fbd
TitleKlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide.
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*AP*(OH3)P*C)-3')
  • DNA (5'-D(P*AP*AP*AP*CP*GP*GP*TP*GP*CP*CP*GP*TP*GP*GP*TP*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 / 5'-3' exonuclease activity / 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: 2.099 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 / struct_conn_type
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_alt_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.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*AP*(OH3)P*C)-3')
C: DNA (5'-D(P*AP*AP*AP*CP*GP*GP*TP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5069
Polymers69,7493
Non-polymers7576
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-30 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.964, 109.964, 91.165
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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*AP*(OH3)P*C)-3')


Mass: 3741.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*AP*AP*CP*GP*GP*TP*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 , 5 types, 170 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-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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 16 % PEG 4000, 0.1 M HEPES, 25 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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→47.616 Å / Num. obs: 72040 / % possible obs: 99.9 % / Redundancy: 5.18 % / Rrim(I) all: 0.073 / Net I/σ(I): 13.91
Reflection shellResolution: 2.099→2.11 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 11669 / Rrim(I) all: 0.873 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.099→47.082 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 3616 5.02 %
Rwork0.1983 --
obs0.2001 72023 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→47.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 581 41 164 4921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074944
X-RAY DIFFRACTIONf_angle_d0.5756801
X-RAY DIFFRACTIONf_dihedral_angle_d16.6742886
X-RAY DIFFRACTIONf_chiral_restr0.04762
X-RAY DIFFRACTIONf_plane_restr0.003820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.12660.3611360.30032626X-RAY DIFFRACTION99
2.1266-2.15570.35611300.29322639X-RAY DIFFRACTION100
2.1557-2.18650.26521160.26972633X-RAY DIFFRACTION100
2.1865-2.21920.3571420.27032630X-RAY DIFFRACTION100
2.2192-2.25380.3181120.26762676X-RAY DIFFRACTION100
2.2538-2.29080.27931450.25942674X-RAY DIFFRACTION100
2.2908-2.33030.32851360.24922576X-RAY DIFFRACTION100
2.3303-2.37270.27541210.25012659X-RAY DIFFRACTION100
2.3727-2.41830.33281040.24292689X-RAY DIFFRACTION100
2.4183-2.46760.24111320.23482618X-RAY DIFFRACTION100
2.4676-2.52130.29421320.23012620X-RAY DIFFRACTION100
2.5213-2.57990.27171600.22722600X-RAY DIFFRACTION100
2.5799-2.64450.28461560.23362682X-RAY DIFFRACTION100
2.6445-2.7160.23341410.22832567X-RAY DIFFRACTION100
2.716-2.79590.26681270.22192688X-RAY DIFFRACTION100
2.7959-2.88610.281580.24382578X-RAY DIFFRACTION100
2.8861-2.98920.3151640.2392633X-RAY DIFFRACTION100
2.9892-3.10890.29751110.23352653X-RAY DIFFRACTION100
3.1089-3.25040.25281450.22562640X-RAY DIFFRACTION100
3.2504-3.42170.25921420.20292615X-RAY DIFFRACTION100
3.4217-3.6360.19991470.18412626X-RAY DIFFRACTION100
3.636-3.91660.20411690.17492605X-RAY DIFFRACTION100
3.9166-4.31050.19791700.16062591X-RAY DIFFRACTION100
4.3105-4.93360.18041190.14392646X-RAY DIFFRACTION100
4.9336-6.21360.20181490.16532630X-RAY DIFFRACTION100
6.2136-47.09390.1771520.17032613X-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)
11.565-0.3713-0.04411.17220.14391.6469-0.0246-0.0355-0.6454-0.21870.0594-0.31640.2-0.0307-0.02620.3668-0.11010.08350.3822-0.02750.564539.4901-40.6866-18.2404
21.88961.069-0.68452.0512-0.23472.37980.2415-0.22810.31320.2394-0.20410.1208-0.94740.1741-0.04070.598-0.01760.03050.2665-0.00680.373737.1195-9.05996.6075
31.58830.46740.16341.7078-0.85742.5204-0.1231-0.10970.08260.01840.29040.2728-0.6414-0.9527-0.13980.42010.1470.01080.61920.06090.306918.4212-20.6178-11.6829
41.6661.01120.02651.6724-0.89861.51060.06520.3997-0.38870.2081-0.3331-0.1546-0.31150.30870.24360.33570.0850.03730.39760.07320.417136.8206-22.90434.0249
50.63180.374-0.25961.94020.82951.366-0.1088-0.1275-0.21560.19510.1851-0.1962-0.082-0.1045-0.10830.3230.04880.02320.43190.06980.344536.3509-24.00695.0893
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 562 )
3X-RAY DIFFRACTION3chain 'A' and (resid 563 through 832 )
4X-RAY DIFFRACTION4chain 'B' and (resid 101 through 112 )
5X-RAY DIFFRACTION5chain 'C' and (resid 204 through 216 )

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