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- PDB-1tau: TAQ POLYMERASE (E.C.2.7.7.7)/DNA/B-OCTYLGLUCOSIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1tau
TitleTAQ POLYMERASE (E.C.2.7.7.7)/DNA/B-OCTYLGLUCOSIDE COMPLEX
Components
  • DNA (5'-D(*CP*GP*GP*AP*TP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*CP*G)-3')
  • PROTEIN (TAQ POLYMERASE)
Keywordstransferase/DNA / PROTEIN-DNA COMPLEX / Taq DNA Polymerase / 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 / 5'-nuclease / 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 polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 5'-nuclease / 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 / 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 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsEom, S.H. / Wang, J. / Steitz, T.A.
Citation
Journal: Nature / Year: 1996
Title: Structure of Taq ploymerase with DNA at the polymerase active site.
Authors: Eom, S.H. / Wang, J. / Steitz, T.A.
#1: Journal: Nature / Year: 1995
Title: Crystal Structure of Thermus Aquatics DNA Polymerase
Authors: Kim, Y. / Eom, S.H. / Wang, J. / Lee, D.-S. / Suh, S.W. / Steitz, T.A.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: Isolation, Characterization, and Expression in Escherichia Coli of the DNA Polymerase Gene From Thermus Aquaticus
Authors: Lawyer, F.C. / Stoffel, S. / Saiki, R.K. / Myambo, K. / Drummond, R. / Gelfand, D.H.
History
DepositionJun 17, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 18, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 1, 2017Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA (5'-D(*GP*CP*GP*AP*TP*CP*CP*G)-3')
P: DNA (5'-D(*CP*GP*GP*AP*TP*CP*GP*C)-3')
A: PROTEIN (TAQ POLYMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2595
Polymers98,9013
Non-polymers3582
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.600, 107.600, 170.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*GP*AP*TP*CP*CP*G)-3')


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*GP*AP*TP*CP*GP*C)-3')


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TAQ POLYMERASE) / E.C.2.7.7.7


Mass: 94046.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase
#4: Sugar ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 800011
3NA CITRATE11
4ZN SULFATE11
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium citrate1drop
24 %(w/v)PEG80001drop
31 mM1dropZnSO4
40-400 mM1dropKCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 21866 / % possible obs: 93.3 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.9
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / % possible obs: 93.3 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.305 -5 %
Rwork0.244 --
obs-16798 -
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6331 322 21 0 6674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.11
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_deg1.87

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