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- PDB-3t3f: Ternary Structure of the large fragment of Taq DNA polymerase bou... -

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Basic information

Entry
Database: PDB / ID: 3t3f
TitleTernary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP
Components
  • 5'-D(*AP*AP*AP*(3DR)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'
  • 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA polymerase / Abasic site / Translesion synthesis / A-rule / base stacking / dNITP / Nitroindol triphosphate / base analogue / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / double-strand break repair via alternative nonhomologous end joining / hydrolase activity, acting on ester bonds / 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 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-N5P / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Authors: Obeid, S. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'
C: 5'-D(*AP*AP*AP*(3DR)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,38926
Polymers69,3693
Non-polymers2,02023
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-63 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.778, 109.778, 91.219
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-80-

HOH

21A-230-

HOH

31A-866-

HOH

41A-868-

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 / Fragment: klenow fragment (UNP residues 293-832)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 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 / Details: DNA primer
#3: DNA chain 5'-D(*AP*AP*AP*(3DR)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'


Mass: 4815.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template

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Non-polymers , 6 types, 341 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-N5P / 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE / 5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE


Mass: 518.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O14P3
#8: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M TRIS HCl, 0.2 M MgFormate, 18% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2011
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 50729 / Num. obs: 50510 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→2.01 Å / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 1.58 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_74model building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.7.1_74phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KTQ

3ktq


Resolution: 1.9→42.155 Å / SU ML: 0.52 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2525 5.03 %Random
Rwork0.1701 ---
obs0.172 50201 99.78 %-
all-50201 --
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3698 Å2-0 Å20 Å2
2--7.3698 Å2-0 Å2
3---1.3147 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 499 127 318 5103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145001
X-RAY DIFFRACTIONf_angle_d1.1946887
X-RAY DIFFRACTIONf_dihedral_angle_d16.171923
X-RAY DIFFRACTIONf_chiral_restr0.074751
X-RAY DIFFRACTIONf_plane_restr0.005795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93660.32641440.27582599X-RAY DIFFRACTION100
1.9366-1.97610.30651370.26752611X-RAY DIFFRACTION100
1.9761-2.01910.3011530.24262589X-RAY DIFFRACTION100
2.0191-2.0660.2511430.22112633X-RAY DIFFRACTION99
2.066-2.11770.25361340.19462597X-RAY DIFFRACTION100
2.1177-2.1750.22821220.18842656X-RAY DIFFRACTION100
2.175-2.2390.24211240.17362645X-RAY DIFFRACTION100
2.239-2.31120.21461390.16972604X-RAY DIFFRACTION100
2.3112-2.39380.22041210.16482671X-RAY DIFFRACTION100
2.3938-2.48970.19181260.16112636X-RAY DIFFRACTION100
2.4897-2.6030.21841510.16092660X-RAY DIFFRACTION100
2.603-2.74020.20421490.16162627X-RAY DIFFRACTION100
2.7402-2.91180.19691380.16322646X-RAY DIFFRACTION100
2.9118-3.13660.2011340.15592670X-RAY DIFFRACTION100
3.1366-3.45210.17231490.15122659X-RAY DIFFRACTION100
3.4521-3.95130.19551590.14472674X-RAY DIFFRACTION100
3.9513-4.97690.1861410.15432705X-RAY DIFFRACTION100
4.9769-42.16530.20481610.19362794X-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)
11.7090.3102-0.2521.5086-0.19381.1578-0.12530.0689-0.4922-0.2597-0.0017-0.42010.4330.19780.11590.1898-0.11970.14070.1655-0.07510.299839.9399-43.6016-17.8851
21.17420.74640.02040.85250.05291.4298-0.07070.03460.1594-0.06990.1186-0.0209-0.5572-0.0363-0.02010.2175-0.04640.04260.08450.03070.145234.216-13.6871-2.7006
34.45371.5998-0.65043.085-2.85332.82520.2107-0.50810.89910.83720.1583-0.0723-1.2422-0.26190.25280.51060.30310.02780.5614-0.02740.36589.7408-13.9953-6.518
41.37730.6363-0.18631.3465-0.57212.5027-0.12570.1998-0.0195-0.10550.13990.103-0.3536-0.6533-0.09840.1479-0.0109-0.00220.27020.02330.080117.8069-25.6389-13.5732
54.7564-0.01580.0791.2742-0.61310.74830.01390.3451-0.27750.1652-0.202-0.1479-0.16610.61050.09310.16040.0348-0.01030.23770.00610.146637.3981-23.29314.4142
60.73110.14770.06212.08670.36222.7912-0.1552-0.196-0.27490.22390.0306-0.30440.02930.0940.10970.10850.0155-0.01850.14750.05070.122237.015-24.32785.4394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 293:433)
2X-RAY DIFFRACTION2chain 'A' and (resseq 434:623)
3X-RAY DIFFRACTION3chain 'A' and (resseq 624:682)
4X-RAY DIFFRACTION4chain 'A' and (resseq 683:832)
5X-RAY DIFFRACTION5chain 'B'
6X-RAY DIFFRACTION6chain 'C'

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