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

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Basic information

Entry
Database: PDB / ID: 5oxj
TitleCrystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair
Components
  • DNA polymerase I, thermostable
  • DNA primer
  • DNA template
KeywordsTRANSFERASE / 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
ACETATE ION / : / Chem-NZI / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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
DepositionSep 6, 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 / 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.ptnr2_symmetry / _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)70,35611
Polymers69,5313
Non-polymers8268
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-20 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.347, 109.347, 90.636
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: 60934.949 Da / Num. of mol.: 1 / Mutation: M747K
Source method: isolated from a genetically manipulated source
Details: Mutant M747K / 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: 4938.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 106 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-NZI / [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate


Mass: 490.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N2O13P3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 45.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% PEG3350 + 0.1M Mg(OAc)2 + 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 2→47.349 Å / Num. obs: 81385 / % possible obs: 99.3 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rrim(I) all: 0.098 / Net I/σ(I): 10.71
Reflection shellResolution: 2→2.12 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 13040 / CC1/2: 0.26 / Rrim(I) all: 1.878 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815: ???)refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3M8S

3m8s


Resolution: 2→47.349 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.43
RfactorNum. reflection% reflection
Rfree0.2573 4101 5.04 %
Rwork0.1961 --
obs0.1992 81358 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→47.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 571 46 98 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085000
X-RAY DIFFRACTIONf_angle_d0.9586886
X-RAY DIFFRACTIONf_dihedral_angle_d16.2372963
X-RAY DIFFRACTIONf_chiral_restr0.051754
X-RAY DIFFRACTIONf_plane_restr0.006840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.02350.44771520.40032593X-RAY DIFFRACTION96
2.0235-2.04810.36671490.37542633X-RAY DIFFRACTION100
2.0481-2.07410.40041410.37152625X-RAY DIFFRACTION99
2.0741-2.10130.34731320.34612707X-RAY DIFFRACTION99
2.1013-2.13010.38761270.33032626X-RAY DIFFRACTION99
2.1301-2.16060.36621220.30552707X-RAY DIFFRACTION99
2.1606-2.19280.33771430.2942696X-RAY DIFFRACTION100
2.1928-2.22710.33471150.30092675X-RAY DIFFRACTION99
2.2271-2.26360.34961330.29972647X-RAY DIFFRACTION100
2.2636-2.30260.3311430.28432669X-RAY DIFFRACTION100
2.3026-2.34450.31931310.28712654X-RAY DIFFRACTION100
2.3445-2.38960.39841160.27372749X-RAY DIFFRACTION100
2.3896-2.43840.31341310.25772690X-RAY DIFFRACTION100
2.4384-2.49140.31611380.24682749X-RAY DIFFRACTION100
2.4914-2.54930.32831660.25192580X-RAY DIFFRACTION99
2.5493-2.61310.2561300.24442627X-RAY DIFFRACTION98
2.6131-2.68370.3371600.24932653X-RAY DIFFRACTION100
2.6837-2.76270.3151410.24852674X-RAY DIFFRACTION100
2.7627-2.85180.33851480.26262673X-RAY DIFFRACTION100
2.8518-2.95380.30251520.26172701X-RAY DIFFRACTION100
2.9538-3.0720.38941330.25322651X-RAY DIFFRACTION100
3.072-3.21180.30151500.21922705X-RAY DIFFRACTION100
3.2118-3.38110.26641340.20582704X-RAY DIFFRACTION100
3.3811-3.59280.23321510.17732646X-RAY DIFFRACTION100
3.5928-3.87010.2241650.1622557X-RAY DIFFRACTION97
3.8701-4.25940.17591730.12792657X-RAY DIFFRACTION100
4.2594-4.87520.18131240.12112712X-RAY DIFFRACTION100
4.8752-6.14010.22341470.14042684X-RAY DIFFRACTION100
6.1401-47.36190.19791540.14022613X-RAY DIFFRACTION98
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)
10.5035-0.16250.0940.36830.50610.74610.0178-0.0379-0.2613-0.19270.0455-0.26750.109-0.0689-00.3411-0.11570.0620.3902-0.02780.552139.4246-41.0541-18.2248
21.09990.9416-0.20780.8058-0.46971.08370.07430.07530.06920.0939-0.0186-0.0062-0.5226-0.32180.01780.44610.04820.02530.3080.010.327832.0395-12.5124-1.5027
30.0438-0.08540.02440.0608-0.030.0027-0.1252-0.13120.3334-0.01610.46780.21030.09160.25-0.00011.04110.2861-0.09090.95150.04480.852911.8823-12.1958-3.7883
40.44940.20840.26510.88420.0150.9703-0.11770.10250.0057-0.13240.22850.0655-0.3287-0.65080.00520.3034-0.0133-0.01680.6280.0450.303717.2322-24.4733-12.7038
50.01980.1476-0.14680.3181-0.39530.4830.00270.3121-0.20260.474-0.4172-0.046-0.47630.258-0.12810.24180.0523-0.00020.53740.11180.484838.1755-23.53795.1394
60.14220.1925-0.15780.4740.2960.4641-0.1755-0.4005-0.33040.23320.0688-0.0672-0.167-0.3352-0.00010.3560.048-0.00920.57170.0830.415132.8724-23.14556.339
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 632 )
3X-RAY DIFFRACTION3chain 'A' and (resid 633 through 681 )
4X-RAY DIFFRACTION4chain 'A' and (resid 682 through 832 )
5X-RAY DIFFRACTION5chain 'B' and (resid 101 through 111 )
6X-RAY DIFFRACTION6chain 'C' and (resid 201 through 216 )

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