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- PDB-6q4v: KlenTaq DNA polymerase in complex with dATP -

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Basic information

Entry
Database: PDB / ID: 6q4v
TitleKlenTaq DNA polymerase in complex with 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 / modified nucleotide KlenTaq DNA polymerase next-generation sequencing
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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsKropp, H.M. / Diederichs, K. / Marx, A.
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)70,2327
Polymers69,6003
Non-polymers6324
Water3,441191
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-23 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.482, 109.482, 91.255
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-1140-

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 , 5 types, 195 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 27 % PEG 4000, 0.2 M ammonium acetate, 0.01 M magnesium (II) acetate, 0.1 M MES pH 6.5

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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: 2.006→47.407 Å / Num. obs: 81683 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rrim(I) all: 0.076 / Net I/σ(I): 11.59
Reflection shellResolution: 2.006→2.016 Å / Redundancy: 5.14 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 12970 / Rrim(I) all: 1.082 / % possible all: 97.8

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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: 2.006→47.407 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25.83
RfactorNum. reflection% reflection
Rfree0.2186 4111 5.04 %
Rwork0.1857 --
obs0.1874 81638 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.006→47.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 566 36 191 5070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035036
X-RAY DIFFRACTIONf_angle_d0.6236937
X-RAY DIFFRACTIONf_dihedral_angle_d15.8532973
X-RAY DIFFRACTIONf_chiral_restr0.04764
X-RAY DIFFRACTIONf_plane_restr0.004818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0056-2.02920.31571360.31732396X-RAY DIFFRACTION90
2.0292-2.05390.2951550.30222640X-RAY DIFFRACTION100
2.0539-2.07990.27021390.28152741X-RAY DIFFRACTION100
2.0799-2.10730.30831360.27882696X-RAY DIFFRACTION100
2.1073-2.13620.28321300.27522644X-RAY DIFFRACTION100
2.1362-2.16670.29851200.26642719X-RAY DIFFRACTION100
2.1667-2.1990.2991420.25612687X-RAY DIFFRACTION100
2.199-2.23340.28011210.2632739X-RAY DIFFRACTION100
2.2334-2.270.27321260.24812654X-RAY DIFFRACTION100
2.27-2.30920.30251570.24032660X-RAY DIFFRACTION100
2.3092-2.35120.30031310.24842713X-RAY DIFFRACTION100
2.3512-2.39640.30511110.2292704X-RAY DIFFRACTION100
2.3964-2.44530.24461330.24152716X-RAY DIFFRACTION100
2.4453-2.49850.2861330.23412683X-RAY DIFFRACTION100
2.4985-2.55660.30741650.22812654X-RAY DIFFRACTION100
2.5566-2.62050.25561320.24242659X-RAY DIFFRACTION100
2.6205-2.69130.31061620.24892683X-RAY DIFFRACTION100
2.6913-2.77050.27141420.23382654X-RAY DIFFRACTION100
2.7705-2.85990.27971500.2382712X-RAY DIFFRACTION100
2.8599-2.96210.26551460.22672711X-RAY DIFFRACTION100
2.9621-3.08070.26461370.21582643X-RAY DIFFRACTION100
3.0807-3.22090.2261490.21632676X-RAY DIFFRACTION100
3.2209-3.39070.21141320.19282705X-RAY DIFFRACTION100
3.3907-3.6030.16611510.17332665X-RAY DIFFRACTION100
3.603-3.88110.22131770.15732660X-RAY DIFFRACTION100
3.8811-4.27150.1541700.14072648X-RAY DIFFRACTION100
4.2715-4.8890.18341250.12332700X-RAY DIFFRACTION100
4.889-6.15750.19581460.13772692X-RAY DIFFRACTION100
6.1575-47.42030.16411570.14112673X-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)
11.7778-0.5546-0.03572.3810.1741.8995-0.09290.0249-0.7152-0.32250.0666-0.54410.4663-0.03730.02140.5246-0.14520.12120.4208-0.05630.67539.7538-41.1164-18.2356
21.58021.0622-0.67021.5004-0.28613.96810.2006-0.03760.24410.0852-0.03940.0076-1.0306-0.4152-0.00010.46510.10140.04220.28370.01670.365831.7154-12.5484-1.5967
30.54580.3069-0.77093.00171.07261.9104-0.0083-0.29010.44180.08560.23450.6348-1.2264-1.4873-0.21320.78590.50110.04611.20460.05270.55718.9987-12.1495-1.8855
41.56250.4288-0.04221.1521-0.02813.9622-0.17190.1863-0.0803-0.37150.26180.1677-0.0021-1.2198-0.10710.2964-0.0243-0.01130.65490.02270.348219.2947-26.5523-15.3742
53.13671.1741.15882.3537-0.41673.62460.14510.4-0.54740.0711-0.3871-0.5409-0.15670.40790.23970.36480.00710.03360.42370.05990.477638.061-23.54465.3123
63.88180.90380.46114.43994.51075.28810.3-0.16940.0481.6566-0.584-0.20440.0178-1.09010.05430.69740.0203-0.04130.76220.02350.407817.7362-21.70167.1696
72.55290.8662-2.37073.00290.79723.1714-0.1592-0.0596-0.41830.29780.3404-0.5134-0.02130.5952-0.21370.31390.0287-0.02760.32310.03620.450239.4408-24.01755.9506
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 633 )
3X-RAY DIFFRACTION3chain 'A' and (resid 634 through 700 )
4X-RAY DIFFRACTION4chain 'A' and (resid 701 through 832 )
5X-RAY DIFFRACTION5chain 'B' and (resid 101 through 111 )
6X-RAY DIFFRACTION6chain 'C' and (resid 201 through 205 )
7X-RAY DIFFRACTION7chain 'C' and (resid 206 through 216 )

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