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- PDB-5nkl: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 5nkl
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP
Components
  • DNA (5'-D(*AP*AP*AP*(DNU)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))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE / DNA polymerase / artificial base pair / unnatural base pair / ternary complex
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
Chem-91R / Chem-91T / 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: 1.7 Å
AuthorsBetz, K. / Marx, A. / Diederichs, K. / Hirao, I. / Kimoto, M.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair.
Authors: Betz, K. / Kimoto, M. / Diederichs, K. / Hirao, I. / Marx, A.
History
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title / _citation_author.name
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_id / _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*(DNU)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,99310
Polymers69,5693
Non-polymers1,4247
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-19 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.777, 108.777, 90.571
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-1231-

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: 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*(DNU)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 5014.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 310 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-91T / [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 566.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N2O16P3
#7: Chemical ChemComp-91R / [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 566.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N2O16P3
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM TRIS pH 8.5, 0.2M Sodium 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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.113 Å / Num. obs: 130009 / % possible obs: 98.4 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rpim(I) all: 0.115 / Net I/σ(I): 8.38
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.47 / Num. unique obs: 20629 / CC1/2: 0.147 / Rpim(I) all: 3.519 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3RTV

3rtv


Resolution: 1.7→47.102 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 6580 5.06 %
Rwork0.1807 --
obs0.1835 129943 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 573 88 303 5255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115141
X-RAY DIFFRACTIONf_angle_d1.1987085
X-RAY DIFFRACTIONf_dihedral_angle_d18.0783030
X-RAY DIFFRACTIONf_chiral_restr0.062771
X-RAY DIFFRACTIONf_plane_restr0.009848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.43842100.38564005X-RAY DIFFRACTION97
1.7193-1.73960.40842210.38314026X-RAY DIFFRACTION97
1.7396-1.76080.43062050.37354112X-RAY DIFFRACTION98
1.7608-1.78310.40722260.37594086X-RAY DIFFRACTION97
1.7831-1.80650.36152010.34154090X-RAY DIFFRACTION98
1.8065-1.83130.36542250.34174038X-RAY DIFFRACTION98
1.8313-1.85750.37722450.32484062X-RAY DIFFRACTION98
1.8575-1.88520.34011990.31154152X-RAY DIFFRACTION98
1.8852-1.91460.36932350.32264028X-RAY DIFFRACTION98
1.9146-1.9460.35682000.29024133X-RAY DIFFRACTION98
1.946-1.97960.32032330.28224081X-RAY DIFFRACTION98
1.9796-2.01560.33142300.27574061X-RAY DIFFRACTION98
2.0156-2.05440.28772300.26474135X-RAY DIFFRACTION98
2.0544-2.09630.29452140.24094087X-RAY DIFFRACTION99
2.0963-2.14190.26941910.22864143X-RAY DIFFRACTION99
2.1419-2.19170.25442050.21544065X-RAY DIFFRACTION99
2.1917-2.24650.28931780.21384217X-RAY DIFFRACTION99
2.2465-2.30720.24852420.20184071X-RAY DIFFRACTION99
2.3072-2.37510.26871740.19954201X-RAY DIFFRACTION99
2.3751-2.45180.24451950.19184127X-RAY DIFFRACTION99
2.4518-2.53940.26042460.18514143X-RAY DIFFRACTION99
2.5394-2.64110.23342290.17554134X-RAY DIFFRACTION99
2.6411-2.76130.26572150.18594119X-RAY DIFFRACTION99
2.7613-2.90680.25092290.20174149X-RAY DIFFRACTION100
2.9068-3.08890.30072110.18924165X-RAY DIFFRACTION99
3.0889-3.32740.23012570.17224114X-RAY DIFFRACTION100
3.3274-3.66210.19282290.14494153X-RAY DIFFRACTION100
3.6621-4.19170.1792590.12914151X-RAY DIFFRACTION100
4.1917-5.280.1852060.11324150X-RAY DIFFRACTION100
5.28-47.11990.18312400.13994165X-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)
10.2866-0.02550.14170.54080.53840.67780.0270.0645-0.1209-0.17490.0288-0.16890.1257-0.02560.00270.3247-0.13270.07090.24-0.02890.340539.304-41.0432-18.2932
20.90350.5834-0.48450.7643-0.38650.64280.0421-0.00070.14520.03160.01230.1416-0.2817-0.00160.00150.3278-0.07580.0320.1756-0.0060.275935.9257-11.0051.7279
30.0148-0.0793-0.01940.47680.10810.1156-0.1317-0.09630.0822-0.03190.18120.0646-0.3397-0.32670.01060.38070.0897-0.04020.62030.09230.272111.8072-13.6388-8.5115
40.354-0.11540.19020.5465-0.29391.2917-0.13790.041-0.0564-0.17890.17880.0151-0.1835-0.5432-0.0280.2667-0.0822-0.01740.47140.0510.235517.4303-24.939-13.3223
50.07380.1198-0.17990.113-0.10590.24560.02480.11930.0230.2015-0.09530.1297-0.30950.4453-0.03230.2074-0.00960.00410.32890.03370.319937.9716-23.38415.3146
60.01820.1217-0.11190.38170.43590.5283-0.2548-0.0886-0.16260.01580.1941-0.0655-0.079-0.1235-0.0010.2656-0.0217-0.00940.33980.04770.276732.5103-22.89616.3047
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 685 )
4X-RAY DIFFRACTION4chain 'A' and (resid 686 through 831 )
5X-RAY DIFFRACTION5chain 'B' and (resid 101 through 111 )
6X-RAY DIFFRACTION6chain 'C' and (resid 201 through 216 )

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