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- PDB-6q4u: KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-... -

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Basic information

Entry
Database: PDB / ID: 6q4u
TitleKlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP
Components
  • DNA (5'-D(*AP*AP*CP*TP*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*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsDNA BINDING PROTEIN / DNA polymerase archaeal B-family modified nucleotide next-generation sequencing
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-HHZ / : / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsKropp, H.M. / Diederichs, K. / Marx, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide.
Authors: Kropp, H.M. / Diederichs, K. / Marx, A.
History
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.title ..._citation.journal_abbrev / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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*GP*GP*CP*CP*AP*(DOC))-3')
C: DNA (5'-D(*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,56510
Polymers69,6003
Non-polymers9657
Water4,792266
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-24 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.359, 109.359, 90.893
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-1004-

HOH

21A-1195-

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*(DOC))-3')


Mass: 3601.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 273 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-HHZ / [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 645.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N5O15P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 14 % PEG 8000, 0.1 M Tris pH 8.0, 0.2 M magnesium formate, 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.005→47.354 Å / Num. obs: 81414 / % possible obs: 99.9 % / Redundancy: 5.26 % / Rrim(I) all: 0.09 / Net I/σ(I): 11.21
Reflection shellResolution: 2.005→2.016 Å / Redundancy: 5.36 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 13148 / Rrim(I) all: 0.849 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(dev_3283: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RTV

3rtv


Resolution: 2.005→47.354 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25
RfactorNum. reflection% reflection
Rfree0.2197 4094 5.03 %
Rwork0.1849 --
obs0.1867 81381 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.005→47.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 566 58 266 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035136
X-RAY DIFFRACTIONf_angle_d0.6157072
X-RAY DIFFRACTIONf_dihedral_angle_d17.3923040
X-RAY DIFFRACTIONf_chiral_restr0.04769
X-RAY DIFFRACTIONf_plane_restr0.003843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0055-2.02910.37611500.33392638X-RAY DIFFRACTION99
2.0291-2.05380.27621410.29632649X-RAY DIFFRACTION100
2.0538-2.07980.26561470.27282688X-RAY DIFFRACTION100
2.0798-2.10720.28581400.28252683X-RAY DIFFRACTION100
2.1072-2.13610.33411230.27322666X-RAY DIFFRACTION100
2.1361-2.16660.34091220.25932716X-RAY DIFFRACTION100
2.1666-2.19890.28031410.25392621X-RAY DIFFRACTION100
2.1989-2.23330.29831170.25522758X-RAY DIFFRACTION100
2.2333-2.26990.28591350.2452615X-RAY DIFFRACTION100
2.2699-2.3090.28921400.24792672X-RAY DIFFRACTION100
2.309-2.3510.26411310.2412675X-RAY DIFFRACTION100
2.351-2.39620.28791160.22432703X-RAY DIFFRACTION100
2.3962-2.44510.21290.23422706X-RAY DIFFRACTION100
2.4451-2.49830.28781300.22312693X-RAY DIFFRACTION100
2.4983-2.55640.26281640.21972584X-RAY DIFFRACTION100
2.5564-2.62030.25461440.22092675X-RAY DIFFRACTION100
2.6203-2.69120.28741520.22112679X-RAY DIFFRACTION100
2.6912-2.77040.21621390.21842655X-RAY DIFFRACTION100
2.7704-2.85980.27621500.22462656X-RAY DIFFRACTION100
2.8598-2.9620.27771520.22692687X-RAY DIFFRACTION100
2.962-3.08050.26941290.21062671X-RAY DIFFRACTION100
3.0805-3.22070.20561480.19882669X-RAY DIFFRACTION100
3.2207-3.39050.24851440.1752655X-RAY DIFFRACTION100
3.3905-3.60280.18011400.16722603X-RAY DIFFRACTION99
3.6028-3.88090.21921790.15742637X-RAY DIFFRACTION100
3.8809-4.27120.1441690.13552633X-RAY DIFFRACTION100
4.2712-4.88870.17841230.12642706X-RAY DIFFRACTION100
4.8887-6.15710.19891440.14112653X-RAY DIFFRACTION100
6.1571-47.3670.1671550.14982641X-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)
11.0074-0.4522-0.05942.26970.05021.6021-0.0330.0162-0.4333-0.29220.0157-0.39760.37490.02020.01530.4819-0.12920.0920.4065-0.05120.518839.8473-41.1178-18.2576
21.81321.0079-0.8861.701-0.29233.66980.3538-0.16620.25960.225-0.17940.055-1.1989-0.1167-0.17360.6122-0.03050.0340.2577-0.00720.36536.7262-8.73226.7396
31.43170.5534-0.10021.6616-0.52393.5975-0.08940.06650.0989-0.1080.1940.2216-0.5403-1.1963-0.08020.34170.1124-0.03390.66430.03090.318618.0317-20.8754-11.7811
43.8937-4.21231.9266.3105-2.45033.66840.14830.536-0.19430.0989-0.4906-0.3864-0.08680.42670.29970.2963-0.05360.00840.35050.04930.422238.1167-23.54515.3173
58.33970.5578-1.10197.81780.36783.09310.27690.01610.0011.6343-0.592-0.6328-0.6652-1.37790.24960.63510.0311-0.08720.65120.06420.331218.1213-21.76147.4499
64.1411.6304-2.87364.19770.78642.9767-0.10640.22-0.430.3470.4132-0.4128-0.14290.6348-0.29320.27530.0341-0.01670.20010.02290.319738.3881-23.1545.2264
78.48555.387-7.37284.2765-4.62448.4716-0.1528-0.5081-0.60610.4320.38850.28870.42980.037-0.12490.50090.23760.14030.89910.48711.048550.6298-33.73113.7305
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 111 )
5X-RAY DIFFRACTION5chain 'C' and (resid 201 through 205 )
6X-RAY DIFFRACTION6chain 'C' and (resid 206 through 215 )
7X-RAY DIFFRACTION7chain 'C' and (resid 216 through 216 )

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