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- PDB-5e41: Crystal structure of the large fragment of DNA Polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 5.0E+41
TitleCrystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate
Components
  • DNA (5'-D(*AP*AP*AP*AP*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 / 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-AUL / 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
DepositionOct 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Jan 10, 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_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_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_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*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,64110
Polymers69,5033
Non-polymers1,1397
Water5,855325
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-21 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.774, 107.774, 89.614
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*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 332 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AUL / 2'-deoxy-5-{(1E)-5-[(10-hydroxydecanoyl)amino]pent-1-en-1-yl}uridine 5'-(tetrahydrogen triphosphate)


Mass: 721.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H42N3O16P3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05M Sodium cacodylate pH 6.5, 0.01M Magnesium acetate, 0.2M 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: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.7 Å / Num. obs: 55908 / % possible obs: 99.9 % / Redundancy: 9.6 % / Net I/σ(I): 13.41

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Processing

Software
NameVersionClassification
PHENIX(dev_2165: ???)refinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3M8S

3m8s


Resolution: 1.8→46.668 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2825 5.05 %
Rwork0.1919 --
obs0.1942 55886 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 569 72 325 5257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065115
X-RAY DIFFRACTIONf_angle_d0.8247041
X-RAY DIFFRACTIONf_dihedral_angle_d15.6233016
X-RAY DIFFRACTIONf_chiral_restr0.047768
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.83120.42991560.42042582X-RAY DIFFRACTION100
1.8312-1.86450.42081420.41192632X-RAY DIFFRACTION100
1.8645-1.90040.42121400.40012626X-RAY DIFFRACTION100
1.9004-1.93920.40741380.38662604X-RAY DIFFRACTION100
1.9392-1.98130.36331470.34112617X-RAY DIFFRACTION100
1.9813-2.02740.33851450.31722651X-RAY DIFFRACTION100
2.0274-2.07810.3251370.30042608X-RAY DIFFRACTION100
2.0781-2.13430.30761210.26322666X-RAY DIFFRACTION100
2.1343-2.19710.31361280.25152665X-RAY DIFFRACTION100
2.1971-2.2680.27291400.23322621X-RAY DIFFRACTION100
2.268-2.34910.28161230.21262652X-RAY DIFFRACTION100
2.3491-2.44310.26931260.20882666X-RAY DIFFRACTION100
2.4431-2.55430.26181500.20132651X-RAY DIFFRACTION100
2.5543-2.6890.29151480.20672637X-RAY DIFFRACTION100
2.689-2.85740.23691370.20612657X-RAY DIFFRACTION100
2.8574-3.0780.26731370.20082671X-RAY DIFFRACTION100
3.078-3.38770.23011490.17832660X-RAY DIFFRACTION100
3.3877-3.87770.19261590.15142679X-RAY DIFFRACTION100
3.8777-4.88460.18491410.13512702X-RAY DIFFRACTION100
4.8846-46.68320.1811610.15182814X-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)
11.33830.1521-0.01782.71570.3571.7796-0.06280.0839-0.3794-0.3095-0.0067-0.37860.54350.05120.06980.5266-0.07740.09170.3084-0.0270.430739.09-40.822-18.3513
21.69110.5159-0.15981.52930.27172.04370.0982-0.19420.2650.1416-0.05830.0066-0.29630.0183-0.04560.3808-0.06210.01740.2693-0.00090.368435.704-10.94791.548
31.44750.0925-0.60171.598-0.74774.3885-0.07750.0310.07580.08050.25470.366-0.2638-1.2145-0.14210.29830.01120.00020.63830.04560.338912.4034-22.0796-7.2508
44.0551.32370.55352.0457-0.49292.6556-0.0830.49850.3618-0.32170.21660.1104-0.558-0.4253-0.10080.5164-0.03320.0080.44190.07550.319424.317-15.7312-24.5371
52.56430.5640.4362.4137-0.77562.19640.01470.0183-0.36720.258-0.206-0.2471-0.13350.72750.21470.3941-0.06110.0040.47220.02260.425937.5979-23.2185.1703
62.2512-0.7043-0.07483.58733.61283.8103-0.1413-1.26250.90161.08990.18710.18580.0093-0.5643-0.09310.57120.01330.03470.8424-0.07050.462717.3431-20.84177.0021
71.003-0.2945-0.76911.45320.87020.7491-0.1358-0.3183-0.11120.19030.2167-0.26310.08050.1714-0.09320.3915-0.0716-0.01250.38530.02940.351339.135-23.83855.9666
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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