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

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Basic information

Entry
Database: PDB / ID: 6fbg
TitleKlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer nucleotide.
Components
  • DNA (5'-D(*AP*AP*AP*CP*GP*CP*CP*GP*GP*TP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*(OH3)P*CP*GP*GP*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 / 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 / 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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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: 1.702 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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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*AP*(OH3)P*CP*GP*GP*C)-3')
C: DNA (5'-D(*AP*AP*AP*CP*GP*CP*CP*GP*GP*TP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73712
Polymers69,7493
Non-polymers9889
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-5 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.288, 109.288, 90.723
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*AP*(OH3)P*CP*GP*GP*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(*AP*AP*AP*CP*GP*CP*CP*GP*GP*TP*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, 275 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


Mass: 62.068 Da / Num. of mol.: 6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 15 % 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: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.702→47.323 Å / Num. obs: 132688 / % possible obs: 99.9 % / Redundancy: 5.17 % / Rrim(I) all: 0.094 / Net I/σ(I): 11.39
Reflection shellResolution: 1.702→1.711 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 21384 / Rrim(I) all: 3.071 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.702→47.323 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 6727 5.07 %
Rwork0.195 --
obs0.1962 132682 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.702→47.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 578 57 266 5092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045040
X-RAY DIFFRACTIONf_angle_d0.5836933
X-RAY DIFFRACTIONf_dihedral_angle_d15.8962950
X-RAY DIFFRACTIONf_chiral_restr0.04766
X-RAY DIFFRACTIONf_plane_restr0.003839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7023-1.72170.43292370.39174174X-RAY DIFFRACTION99
1.7217-1.74190.40482110.38754188X-RAY DIFFRACTION100
1.7419-1.76320.35232220.36954201X-RAY DIFFRACTION100
1.7632-1.78550.38892280.36214148X-RAY DIFFRACTION100
1.7855-1.8090.34211970.35264206X-RAY DIFFRACTION100
1.809-1.83380.33922320.33964165X-RAY DIFFRACTION100
1.8338-1.860.36522480.33444220X-RAY DIFFRACTION100
1.86-1.88770.34782410.32114173X-RAY DIFFRACTION100
1.8877-1.91720.30912200.30634249X-RAY DIFFRACTION100
1.9172-1.94870.30992020.29134169X-RAY DIFFRACTION100
1.9487-1.98230.31652440.29174213X-RAY DIFFRACTION100
1.9823-2.01830.29992500.27854185X-RAY DIFFRACTION100
2.0183-2.05710.29042240.26594218X-RAY DIFFRACTION100
2.0571-2.09910.26152150.24954180X-RAY DIFFRACTION100
2.0991-2.14480.25672080.23564220X-RAY DIFFRACTION100
2.1448-2.19460.24662090.21464224X-RAY DIFFRACTION100
2.1946-2.24950.25331830.21184203X-RAY DIFFRACTION100
2.2495-2.31030.25282350.21094201X-RAY DIFFRACTION100
2.3103-2.37830.22891870.20174263X-RAY DIFFRACTION100
2.3783-2.45510.22541990.19534238X-RAY DIFFRACTION100
2.4551-2.54280.26572500.19684166X-RAY DIFFRACTION100
2.5428-2.64460.21662280.18334166X-RAY DIFFRACTION100
2.6446-2.7650.21792190.18514201X-RAY DIFFRACTION100
2.765-2.91070.20542310.17774226X-RAY DIFFRACTION100
2.9107-3.09310.20362150.17824209X-RAY DIFFRACTION100
3.0931-3.33180.1922480.17084191X-RAY DIFFRACTION100
3.3318-3.6670.16452350.1574163X-RAY DIFFRACTION100
3.667-4.19740.16162580.15434184X-RAY DIFFRACTION100
4.1974-5.28710.19072110.15354217X-RAY DIFFRACTION100
5.2871-47.34140.19582400.17984194X-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)
10.7726-0.121-0.36392.5363-0.2291.5342-0.07230.0487-0.4094-0.1814-0.0135-0.44740.22210.12290.07720.2954-0.06860.09060.3319-0.08430.460139.4294-41.2218-18.149
21.55880.8366-0.44331.5089-0.10692.4620.1679-0.13780.20650.1517-0.03980.0594-0.65420.0664-0.10950.3247-0.00490.04710.2095-0.00350.28236.1-11.1891.7224
31.78020.301-0.63951.45930.06442.3428-0.0303-0.10560.22560.13150.17260.3053-0.7608-0.7333-0.10250.4520.21450.01280.55250.06030.278912.1507-13.6788-8.1192
41.23190.5839-0.20451.0955-0.62892.6431-0.03620.142-0.0141-0.04570.18440.1072-0.2596-0.5648-0.12190.21740.02540.01320.3740.0130.23417.5484-25.2374-12.9245
50.88380.46641.67162.3188-1.15925.32620.06460.2561-0.24460.0445-0.2595-0.24620.06370.33780.15040.2908-0.00530.05590.34010.0220.368336.8718-23.16884.1864
65.37675.23574.76688.25064.25064.2656-0.2064-1.6170.95861.507-0.30810.41260.3429-0.52960.46040.55920.13140.00440.8587-0.0470.42217.8221-21.05167.3503
73.56750.6269-2.09943.58210.78211.7182-0.1763-0.248-0.17610.38720.2986-0.554-0.00450.5841-0.16860.29930.0394-0.02090.30140.00730.331639.9317-24.15476.0506
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 831 )
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 216 )

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