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- PDB-5ytc: Large fragment of DNA Polymerase I from Thermus aquaticus in a cl... -

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Basic information

Entry
Database: PDB / ID: 5ytc
TitleLarge fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site
Components
  • DNA (5'-D(*AP*AP*AP*(92F)P*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)P*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA / REPLICATION / TRANSFERASE-DNA complex
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
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: 2.28 Å
AuthorsZeng, H. / Mondal, M. / Song, R.Y. / Zhang, J. / Xia, B. / Yi, C.Q.
Funding support China, 2items
OrganizationGrant numberCountry
the National Basic Research Foundation of China Grant2014CB964900 China
the National Natural Science Foundation of China Grants31270838 and 21522201 China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.
Authors: Zeng, H. / Mondal, M. / Song, R. / Zhang, J. / Xia, B. / Liu, M. / Zhu, C. / He, B. / Gao, Y.Q. / Yi, C.
History
DepositionNov 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 22, 2022Group: Data collection / Database references / Derived calculations
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.mon_nstd_flag / _database_2.pdbx_DOI ..._chem_comp.mon_nstd_flag / _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
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)P*(DOC))-3')
C: DNA (5'-D(*AP*AP*AP*(92F)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2966
Polymers69,7573
Non-polymers5403
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-25 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.886, 108.886, 90.533
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: 60865.887 Da / Num. of mol.: 1 / Fragment: large fragment
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)P*(DOC))-3')


Mass: 3890.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*(92F)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 5000.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 265 molecules

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


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


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


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 8.5
Details: 0.2 M Mg(HCOO)2, 0.1 M Tris HCl (pH 8.5), 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.28→94.3 Å / Num. obs: 25784 / % possible obs: 98 % / Redundancy: 5.1 % / Net I/σ(I): 19.27
Reflection shellResolution: 2.28→2.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DFK

4dfk


Resolution: 2.28→94.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.207 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.272 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 1453 5.3 %RANDOM
Rwork0.19412 ---
obs0.19742 25784 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å20 Å2
2---0.29 Å20 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 2.28→94.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 573 33 262 5134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0185048
X-RAY DIFFRACTIONr_bond_other_d0.0020.024616
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.896966
X-RAY DIFFRACTIONr_angle_other_deg1.014310593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0175544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8622.108204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61915756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.861555
X-RAY DIFFRACTIONr_chiral_restr0.0780.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021174
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4351.6982161
X-RAY DIFFRACTIONr_mcbond_other0.4341.6972160
X-RAY DIFFRACTIONr_mcangle_it0.7822.5452701
X-RAY DIFFRACTIONr_mcangle_other0.7822.5462702
X-RAY DIFFRACTIONr_scbond_it0.4661.782885
X-RAY DIFFRACTIONr_scbond_other0.4651.782885
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8222.654262
X-RAY DIFFRACTIONr_long_range_B_refined2.67114.4266068
X-RAY DIFFRACTIONr_long_range_B_other2.52414.4375986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.281→2.341 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 109 -
Rwork0.244 1289 -
obs--67.02 %
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)
10.4757-0.5581-0.11551.7473-0.12.03310.056-0.02980.0958-0.0236-0.0032-0.1301-0.23470.3202-0.05290.1731-0.010.0340.0563-0.00670.0229-34.7349-12.41375.3456
20.4276-0.3331-1.2143.3872-0.00553.7647-0.06740.0759-0.01180.06420.15140.47470.198-0.3185-0.0840.0767-0.01550.01560.0826-0.00240.089-38.2916-20.498819.1208
30.6844-1.464-0.32774.4258-1.62594.7568-0.0476-0.16090.17190.36670.0985-0.4071-0.44780.2492-0.05080.1364-0.0629-0.00390.2445-0.01280.0513-36.2115-16.827921.3152
42.15520.2842-1.2860.6012.538213.81470.5780.2848-0.10730.18610.0014-0.15490.2113-0.2981-0.57940.33170.0044-0.00390.17190.01240.185-24.9868-6.96135.8403
50.6006-0.2879-0.01380.9025-0.06091.33860.0421-0.08680.0136-0.08160.01150.0239-0.06770.078-0.05360.19110.00720.00970.094-0.02580.0849-37.584-15.12646.7507
60000000000000-0.000200.2666-0.2267-0.05690.8750.04820.1233-25.1706-11.31031.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A294 - 832
2X-RAY DIFFRACTION2B101 - 111
3X-RAY DIFFRACTION2B113
4X-RAY DIFFRACTION3C201 - 216
5X-RAY DIFFRACTION4A902
6X-RAY DIFFRACTION5A1001 - 1207
7X-RAY DIFFRACTION5B301 - 325
8X-RAY DIFFRACTION5C301 - 330
9X-RAY DIFFRACTION6A903

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