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- PDB-3rr8: Ternary Structure of the large fragment of Taq DNA polymerase bou... -

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Basic information

Entry
Database: PDB / ID: 3rr8
TitleTernary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP
Components
  • (5'-D(*AP*AP*AP*(3DR)P*CP*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*(DDG))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA polymerase / Abasic site / Translesion synthesis / A-rule / 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 / 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 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Sep 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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*(DDG))-3')
C: (5'-D(*AP*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2298
Polymers69,3693
Non-polymers8605
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-4 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.965, 108.965, 90.406
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-83-

HOH

21A-90-

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
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*(DDG))-3')


Mass: 3657.395 Da / Num. of mol.: 1 / Fragment: DNA primer / Source method: obtained synthetically
#3: DNA chain (5'-D(*AP*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4775.082 Da / Num. of mol.: 1 / Fragment: DNA template / Source method: obtained synthetically

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Non-polymers , 3 types, 106 molecules

#4: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0007 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 213727 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.54 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.61
Reflection shellResolution: 2.38→2.53 Å / Redundancy: 8.01 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.61 / Num. unique all: 31236 / % possible all: 97.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: dev_613)model building
PHENIX(phenix.refine: dev_613)refinement
XDSdata reduction
PHENIXdev_613phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LWL

3lwl


Resolution: 2.4→47.183 Å / SU ML: 0.36 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1274 5.18 %Random
Rwork0.2007 ---
obs0.2035 24603 99.93 %-
all-24603 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.305 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.0893 Å20 Å2-0 Å2
2--20.0893 Å2-0 Å2
3---5.3563 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 520 54 101 4882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024925
X-RAY DIFFRACTIONf_angle_d0.6816769
X-RAY DIFFRACTIONf_dihedral_angle_d17.0851905
X-RAY DIFFRACTIONf_chiral_restr0.043745
X-RAY DIFFRACTIONf_plane_restr0.003787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.32791240.26242554X-RAY DIFFRACTION100
2.4962-2.60980.341520.25912545X-RAY DIFFRACTION100
2.6098-2.74730.31451400.25772577X-RAY DIFFRACTION100
2.7473-2.91940.32151400.242553X-RAY DIFFRACTION100
2.9194-3.14480.29041280.24122606X-RAY DIFFRACTION100
3.1448-3.46120.28631380.21862573X-RAY DIFFRACTION100
3.4612-3.96180.23361600.18832579X-RAY DIFFRACTION100
3.9618-4.99060.22651360.16152625X-RAY DIFFRACTION100
4.9906-47.19230.20361560.17052717X-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)
10.0430.0612-0.0210.0292-0.02430.0174-0.05390.0656-0.18620.01030.0408-0.0742-0.0337-0.0469-0.0203-0.0757-0.20890.1232-0.0971-0.0515-0.151436.1455-25.9795-9.1776
20.0120.0055-0.00250.0029-0.00120.00080.015-0.0030.00180.0695-0.0001-0.0035-0.032-0.0383-0.0080.30940.17910.00940.44510.04940.12455.5405-15.5529-3.4188
30.03090.00670.03150.00510.00710.0287-0.0337-0.0213-0.0371-0.02930.01790.0228-0.0207-0.0417-0.03110.0538-0.14110.04390.23410.0207-0.040520.0486-26.1181-15.5521
40.00430.006-0.00360.01320.00190.0101-0.00130.01320.00060.0037-0.0037-0.0024-0.0105-0.0108-0.00430.0180.0512-0.060.09180.03170.097936.6457-23.01954.1336
50.06520.02130.00780.01910.01090.0072-0.0249-0.0013-0.01040.0173-0.006-0.01220.01150.0242-0.01650.00140.0434-0.07130.0580.01770.05435.2117-24.0425.9699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 293:626)
2X-RAY DIFFRACTION2(chain A and resid 627:705)
3X-RAY DIFFRACTION3(chain A and resid 706:832)
4X-RAY DIFFRACTION4(chain B)
5X-RAY DIFFRACTION5(chain C)

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