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- PDB-4dlg: Ternary Structure of the large Fragment of Taq DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 4dlg
TitleTernary Structure of the large Fragment of Taq DNA polymerase
Components
  • DNA polymerase I, thermostable
  • DNA primerPrimer (molecular biology)
  • DNA template
KeywordsTransferase/DNA / DNA polymerase / ternary complex / A family / DNA synthesis / Transferase-DNA complex
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / 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
ACETATE ION / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S. / Holzberger, B.
CitationJournal: Chem Sci / Year: 2012
Title: Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of protein
Authors: Holzberger, B. / Obeid, S. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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_site
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.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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: DNA primer
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,47212
Polymers69,5193
Non-polymers9539
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-30 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.784, 107.784, 89.554
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-906-

ACT

21A-906-

ACT

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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: UNP residues 293-832
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 primer / Primer (molecular biology)


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA template


Mass: 4964.216 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 454 molecules

#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM Na cacodylate, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 15% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.23 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2011
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 47964 / Num. obs: 47964 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.89→2.01 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 1.13 / % possible all: 97.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KTQ

3ktq


Resolution: 1.89→46.672 Å / SU ML: 0.23 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 4647 5.04 %Random
Rwork0.214 ---
obs0.2159 47964 99.48 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.862 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1501 Å20 Å20 Å2
2--1.1501 Å2-0 Å2
3----2.3002 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 531 59 445 5326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055198
X-RAY DIFFRACTIONf_angle_d0.6287190
X-RAY DIFFRACTIONf_dihedral_angle_d14.7012062
X-RAY DIFFRACTIONf_chiral_restr0.041780
X-RAY DIFFRACTIONf_plane_restr0.003853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.91510.39061190.40642559X-RAY DIFFRACTION86
1.9151-1.93760.41271660.36952838X-RAY DIFFRACTION99
1.9376-1.96130.36021560.34982950X-RAY DIFFRACTION100
1.9613-1.98610.34281830.31452854X-RAY DIFFRACTION100
1.9861-2.01220.39461540.3142958X-RAY DIFFRACTION100
2.0122-2.03980.28991630.30352921X-RAY DIFFRACTION100
2.0398-2.06890.28081400.28052984X-RAY DIFFRACTION100
2.0689-2.09980.3151420.26832931X-RAY DIFFRACTION100
2.0998-2.13260.2741330.25512935X-RAY DIFFRACTION100
2.1326-2.16760.29721550.25912902X-RAY DIFFRACTION100
2.1676-2.2050.27151290.24913001X-RAY DIFFRACTION100
2.205-2.24510.31411530.22782990X-RAY DIFFRACTION100
2.2451-2.28820.25021630.22952904X-RAY DIFFRACTION100
2.2882-2.33490.25841400.23432962X-RAY DIFFRACTION100
2.3349-2.38570.34081190.24042913X-RAY DIFFRACTION100
2.3857-2.44120.27411430.23862941X-RAY DIFFRACTION100
2.4412-2.50220.29771840.23062938X-RAY DIFFRACTION100
2.5022-2.56990.27671460.23522925X-RAY DIFFRACTION100
2.5699-2.64550.31371710.23212964X-RAY DIFFRACTION100
2.6455-2.73090.23011530.21892879X-RAY DIFFRACTION100
2.7309-2.82850.26021650.23782936X-RAY DIFFRACTION100
2.8285-2.94170.29351840.22922882X-RAY DIFFRACTION100
2.9417-3.07560.28871180.22793008X-RAY DIFFRACTION100
3.0756-3.23770.26311770.21052911X-RAY DIFFRACTION100
3.2377-3.44050.21781500.18652940X-RAY DIFFRACTION100
3.4405-3.7060.21161820.17132910X-RAY DIFFRACTION100
3.706-4.07880.18491770.16482896X-RAY DIFFRACTION100
4.0788-4.66850.1921580.14422964X-RAY DIFFRACTION100
4.6685-5.880.20641550.16512899X-RAY DIFFRACTION100
5.88-46.6860.20951690.17292932X-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)
10.9799-0.3228-0.03522.14060.44621.1932-0.01270.0527-0.2063-0.10780.0138-0.18930.25270.1258-0.00190.18670.00280.01710.138-0.0040.143239.3981-41.1208-18.5918
20.95190.62270.48671.38510.5371.18140.0442-0.16290.21570.1316-0.09390.1162-0.14470.0040.04660.1426-0.03140.01920.1057-0.01410.172335.4252-10.84071.7706
31.57750.6702-0.24760.8261-1.20993.0971-0.2085-0.70570.65610.48230.23220.2377-1.506-0.9131-0.13210.380.2323-0.03310.6104-0.04780.344711.3008-13.8795-8.5307
41.16590.32540.06061.447-0.7763.0719-0.12010.0750.06120.08570.23060.1137-0.1807-0.8386-0.07440.08670-0.01810.1375-00.068617.516-24.6616-13.447
56.1797-0.77232.38781.4448-0.97592.63060.1485-0.0165-0.48020.3291-0.1833-0.10080.09060.34150.05170.2441-0.0784-0.03440.18910.03010.226736.3316-22.88924.1649
63.25460.64092.2212.85670.36922.6293-0.0952-0.4525-0.03690.32730.0404-0.1428-0.0273-0.05860.03360.192-0.031-0.00040.19030.00750.071634.1943-23.70125.5739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 293:452)
2X-RAY DIFFRACTION2chain 'A' and (resseq 453:603)
3X-RAY DIFFRACTION3chain 'A' and (resseq 604:685)
4X-RAY DIFFRACTION4chain 'A' and (resseq 686:832)
5X-RAY DIFFRACTION5chain 'B'
6X-RAY DIFFRACTION6chain 'C'

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