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

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Basic information

Entry
Database: PDB / ID: 3rrg
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 / 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'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / 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: (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)70,1278
Polymers69,3693
Non-polymers7575
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-20 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.279, 110.279, 90.966
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-144-

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: pET21-b / 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 , 5 types, 145 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
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, 28% 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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 284045 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.96 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 13.69
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 9.82 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 1.52 / Num. unique all: 44153 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: dev_704)model building
PHENIX(phenix.refine: dev_704)refinement
XDSdata reduction
PHENIXdev_704phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LWL

3lwl


Resolution: 2.3→47.752 Å / SU ML: 0.66 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 2813 5.12 %random
Rwork0.1976 ---
obs0.2003 54951 99.99 %-
all-54951 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2457 Å2-0 Å2-0 Å2
2--4.2457 Å2-0 Å2
3----1.9032 Å2
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 499 47 140 4912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034938
X-RAY DIFFRACTIONf_angle_d0.8286789
X-RAY DIFFRACTIONf_dihedral_angle_d16.7061911
X-RAY DIFFRACTIONf_chiral_restr0.051745
X-RAY DIFFRACTIONf_plane_restr0.003796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33970.32111320.31322606X-RAY DIFFRACTION100
2.3397-2.38230.29741240.28852613X-RAY DIFFRACTION100
2.3823-2.42810.26921040.27362627X-RAY DIFFRACTION100
2.4281-2.47770.31341320.27472597X-RAY DIFFRACTION100
2.4777-2.53150.33581330.2652623X-RAY DIFFRACTION100
2.5315-2.59040.32231560.27682608X-RAY DIFFRACTION100
2.5904-2.65520.35341560.27012581X-RAY DIFFRACTION100
2.6552-2.7270.3181390.26842615X-RAY DIFFRACTION100
2.727-2.80720.29371290.23982645X-RAY DIFFRACTION100
2.8072-2.89780.30941480.23732600X-RAY DIFFRACTION100
2.8978-3.00140.26131760.21362547X-RAY DIFFRACTION100
3.0014-3.12150.2787980.22222664X-RAY DIFFRACTION100
3.1215-3.26350.27561480.20552609X-RAY DIFFRACTION100
3.2635-3.43560.26061420.20072607X-RAY DIFFRACTION100
3.4356-3.65070.2321510.18712594X-RAY DIFFRACTION100
3.6507-3.93250.24881650.1812578X-RAY DIFFRACTION100
3.9325-4.3280.21471650.15452608X-RAY DIFFRACTION100
4.328-4.95370.19211140.14092606X-RAY DIFFRACTION100
4.9537-6.2390.21071510.16232615X-RAY DIFFRACTION100
6.239-47.76250.18861500.14532595X-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)
10.73190.2326-0.0370.3105-0.15810.3124-0.09680.1112-0.4674-0.17510.1031-0.2820.1846-0.01680.26750.1328-0.24990.2810.2093-0.17370.625841.834-43.6623-17.7206
20.69540.34690.03010.5783-0.29010.745-0.11170.1244-0.05480.09920.0057-0.0395-0.3539-0.19190.05190.2602-0.09440.03980.16-0.01490.11735.1244-14.5851-1.7643
31.66660.44270.03950.7611-0.25861.4417-0.0705-0.23590.1597-0.02260.14770.1925-0.4585-0.57430.0310.30080.0869-0.00940.67910.07580.135110.9087-16.3015-15.8915
40.52690.15690.00670.87490.69871.11220.0765-0.17140.1160.27990.10070.0625-0.4408-0.0713-0.03430.55940.24740.04730.96030.05530.25587.5795-16.48180.782
50.43470.2794-0.01820.43630.13250.5715-0.17990.1733-0.0336-0.23760.14640.0344-0.0413-0.348-0.28840.0879-0.18470.07160.55060.073-0.020120.3441-26.2529-15.9052
60.6235-0.0308-0.01990.33320.09070.47220.08530.1256-0.13330.0252-0.0845-0.2740.04560.2078-0.01350.07520.1479-0.10350.31390.05610.256237.1969-23.43944.1306
70.48550.38940.26790.5796-0.03271.1575-0.126-0.1737-0.10430.22810.0848-0.18060.07520.0576-0.05190.16590.111-0.09050.26690.06210.245937.4065-24.41365.4707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 294:424)
2X-RAY DIFFRACTION2(chain A and resid 425:600)
3X-RAY DIFFRACTION3(chain A and resid 601:651)
4X-RAY DIFFRACTION4(chain A and resid 652:705)
5X-RAY DIFFRACTION5(chain A and resid 706:832)
6X-RAY DIFFRACTION6(chain B)
7X-RAY DIFFRACTION7(chain C)

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