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- PDB-5szt: Crystal structure of the large fragment of DNA Polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 5szt
TitleCrystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP
Components
  • DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE / linker-modified nucleotide / 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-72J / ACETATE ION / 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
AuthorsHottin, A. / Betz, K. / Marx, A.
CitationJournal: Chemistry / Year: 2017
Title: Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides.
Authors: Hottin, A. / Betz, K. / Diederichs, K. / Marx, A.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _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*GP*CP*(DOC))-3')
C: DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,73013
Polymers69,4943
Non-polymers1,23710
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-29 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.425, 108.425, 90.615
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: 60936.965 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*GP*CP*(DOC))-3')


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*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 , 5 types, 260 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-72J / 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP


Mass: 743.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H44N5O14P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium acetate, 0.2 M ammonium acetate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.95 Å / Num. obs: 57320 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2443)refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3M8S

3m8s


Resolution: 1.8→46.949 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7
RfactorNum. reflection% reflection
Rfree0.2295 2894 5.05 %
Rwork0.1936 --
obs0.1954 57294 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 568 85 244 5188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035228
X-RAY DIFFRACTIONf_angle_d0.6347209
X-RAY DIFFRACTIONf_dihedral_angle_d18.1573105
X-RAY DIFFRACTIONf_chiral_restr0.041776
X-RAY DIFFRACTIONf_plane_restr0.003871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7996-1.82910.38331410.39962543X-RAY DIFFRACTION100
1.8291-1.86070.38411520.38082574X-RAY DIFFRACTION100
1.8607-1.89450.34661280.35462552X-RAY DIFFRACTION100
1.8945-1.9310.39861400.34622566X-RAY DIFFRACTION100
1.931-1.97040.35151390.31832567X-RAY DIFFRACTION100
1.9704-2.01320.31011460.29572559X-RAY DIFFRACTION100
2.0132-2.060.29361380.2742555X-RAY DIFFRACTION100
2.06-2.11160.28951320.25882583X-RAY DIFFRACTION100
2.1116-2.16870.2611210.23112581X-RAY DIFFRACTION100
2.1687-2.23250.31811180.23322583X-RAY DIFFRACTION100
2.2325-2.30450.30271410.22652561X-RAY DIFFRACTION100
2.3045-2.38690.29931150.21152613X-RAY DIFFRACTION100
2.3869-2.48250.26181260.21212606X-RAY DIFFRACTION100
2.4825-2.59540.28091450.20172561X-RAY DIFFRACTION100
2.5954-2.73220.23141460.19842584X-RAY DIFFRACTION100
2.7322-2.90340.22171370.19652595X-RAY DIFFRACTION100
2.9034-3.12750.22631320.19362606X-RAY DIFFRACTION100
3.1275-3.44220.19851440.17542606X-RAY DIFFRACTION100
3.4422-3.94010.19371580.16272622X-RAY DIFFRACTION100
3.9401-4.96320.18611390.13832642X-RAY DIFFRACTION100
4.9632-46.96540.19221560.16942741X-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)
11.2189-0.4172-0.11612.16910.21031.6994-0.04490.0327-0.3981-0.2261-0.0225-0.32410.4850.03020.05950.5104-0.10320.09450.3225-0.03970.447139.2369-41.0134-18.2185
21.25030.7722-0.22611.65860.05173.02190.1231-0.13710.19070.1479-0.05750.0476-0.66140.0165-0.0560.3539-0.03620.02710.2282-0.01420.317535.9026-10.80931.4273
31.26710.3206-0.31051.8284-0.8243.4467-0.0813-0.04720.01270.07630.26720.3522-0.3181-1.3019-0.1250.28820.0435-0.01150.76920.05080.330212.4862-22.3974-7.5443
44.13081.5052-0.43152.2292-0.453.0807-0.09740.51450.2831-0.30480.18310.063-0.4151-0.5422-0.09170.4672-0.028-0.0010.440.04570.291524.2248-15.9511-24.8686
52.8957-0.2571.78191.6928-1.11132.14510.03010.3477-0.38360.2888-0.2886-0.101-0.00230.62060.23440.38890.00460.02740.37420.03650.463237.8865-23.23755.2894
65.4964-0.75610.88092.62860.73784.1263-0.1433-1.23640.4221.0657-0.50790.0915-0.2816-0.97230.47970.5687-0.01510.00790.8422-0.0490.41617.2714-21.20727.1997
71.6050.0576-1.09612.34321.21631.4107-0.0538-0.1449-0.37130.34440.3064-0.51920.02170.3789-0.29870.3264-0.0409-0.04240.31830.0360.396739.2773-23.82035.9964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 452 )
2X-RAY DIFFRACTION2chain 'A' and (resid 453 through 603 )
3X-RAY DIFFRACTION3chain 'A' and (resid 604 through 775 )
4X-RAY DIFFRACTION4chain 'A' and (resid 776 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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