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- PDB-5o7t: Crystal structure of KlenTaq mutant M747K in a closed ternary com... -

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Basic information

Entry
Database: PDB / ID: 5o7t
TitleCrystal structure of KlenTaq mutant M747K in a closed ternary complex with a dG:dCTP base pair
Components
  • DNA polymerase I, thermostable
  • DNA primer
  • DNA template
KeywordsTRANSFERASE / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsBetz, K. / Diederichs, K. / Marx, A.
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase.
Authors: Betz, K. / Nilforoushan, A. / Wyss, L.A. / Diederichs, K. / Sturla, S.J. / Marx, A.
History
DepositionJun 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 / refine_hist / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _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 primer
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1498
Polymers69,5173
Non-polymers6325
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-28 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.476, 109.476, 91.390
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-1171-

HOH

21A-1180-

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: 60934.949 Da / Num. of mol.: 1 / Mutation: M747K
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 primer


Mass: 3657.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA template


Mass: 4924.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 270 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG 3350, 0 .1M Magnesiumacetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999975 Å / Relative weight: 1
ReflectionResolution: 1.8→47.405 Å / Num. obs: 112020 / % possible obs: 98.2 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rrim(I) all: 0.085 / Net I/σ(I): 11.06
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 17660 / CC1/2: 0.169 / Rrim(I) all: 2.875 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3M8S

3m8s


Resolution: 1.8→47.404 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 28.45
RfactorNum. reflection% reflection
Rfree0.2348 5694 5.08 %
Rwork0.1769 --
obs0.1799 112015 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 570 37 265 5164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125063
X-RAY DIFFRACTIONf_angle_d1.2416976
X-RAY DIFFRACTIONf_dihedral_angle_d16.3242992
X-RAY DIFFRACTIONf_chiral_restr0.066765
X-RAY DIFFRACTIONf_plane_restr0.009832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7975-1.81790.40321590.39033217X-RAY DIFFRACTION90
1.8179-1.83930.38971960.3723489X-RAY DIFFRACTION97
1.8393-1.86170.37382270.36293538X-RAY DIFFRACTION98
1.8617-1.88530.35071880.33993506X-RAY DIFFRACTION98
1.8853-1.91010.38741670.32963513X-RAY DIFFRACTION97
1.9101-1.93630.36391990.32223543X-RAY DIFFRACTION98
1.9363-1.96390.35361850.31773492X-RAY DIFFRACTION98
1.9639-1.99320.33522010.30243570X-RAY DIFFRACTION98
1.9932-2.02440.322040.28383517X-RAY DIFFRACTION98
2.0244-2.05760.32021890.28113498X-RAY DIFFRACTION98
2.0576-2.0930.28651810.27823562X-RAY DIFFRACTION98
2.093-2.13110.28491870.26363580X-RAY DIFFRACTION98
2.1311-2.17210.32571550.243528X-RAY DIFFRACTION98
2.1721-2.21640.32231910.24193587X-RAY DIFFRACTION99
2.2164-2.26460.32251430.22763604X-RAY DIFFRACTION99
2.2646-2.31730.26522080.21253506X-RAY DIFFRACTION99
2.3173-2.37530.23871750.21643589X-RAY DIFFRACTION99
2.3753-2.43950.25571450.19983585X-RAY DIFFRACTION98
2.4395-2.51130.25571850.18573561X-RAY DIFFRACTION99
2.5113-2.59230.25712080.18713581X-RAY DIFFRACTION99
2.5923-2.68490.2862040.19843569X-RAY DIFFRACTION99
2.6849-2.79240.23371870.19693541X-RAY DIFFRACTION99
2.7924-2.91950.28982060.21043580X-RAY DIFFRACTION99
2.9195-3.07340.26471970.19413562X-RAY DIFFRACTION99
3.0734-3.26590.25591940.18543588X-RAY DIFFRACTION99
3.2659-3.5180.21031890.16133589X-RAY DIFFRACTION99
3.518-3.87190.22542240.14943547X-RAY DIFFRACTION99
3.8719-4.43180.18712140.12043576X-RAY DIFFRACTION99
4.4318-5.58220.17691830.11283597X-RAY DIFFRACTION100
5.5822-47.4210.16742030.13153606X-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)
10.4733-0.312-0.03880.45830.26690.6291-0.07740.0677-0.4526-0.12970.0803-0.24160.1149-0.0092-0.00770.291-0.10090.10050.3049-0.0620.585239.8719-42.9763-18.0055
20.95610.7813-0.29840.5734-0.35280.54830.1298-0.02660.11310.0212-0.1020.047-0.55530.004-0.00110.4913-0.01390.05940.2446-0.00120.32236.7829-10.99752.4878
30.73840.2452-0.03110.56080.04261.0412-0.03830.0866-0.043-0.12310.04950.0137-0.2394-0.39770.00050.31910.05280.01330.46610.05650.271318.1101-20.1885-11.6504
40.03090.1573-0.02850.1875-0.08070.11510.02710.1889-0.00180.2331-0.2056-0.1412-0.37010.1294-00.2860.03570.010.34470.06830.38238.1174-23.64085.1568
50.32710.1246-0.12580.3807-0.0350.0499-0.2027-0.12660.020.5541-0.1923-0.4532-0.1854-0.0363-0.02260.41150.0556-0.06220.54650.07290.235517.7724-21.17897.2707
60.04410.0741-0.10.26650.20740.2567-0.09370.084-0.56420.1180.3872-0.2028-0.07920.13280.00490.27870.0330.00050.33780.04610.350138.4531-23.20145.0931
70.0880.2134-0.18530.5146-0.44270.38-0.1546-0.0176-0.02280.150.00460.05760.07980.0668-0.05760.34190.18510.05560.43410.380.889350.8867-33.840113.4393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 433 )
2X-RAY DIFFRACTION2chain 'A' and (resid 434 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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