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- PDB-3rr7: Binary Structure of the large fragment of Taq DNA polymerase boun... -

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Basic information

Entry
Database: PDB / ID: 3rr7
TitleBinary Structure of the large fragment of Taq DNA polymerase bound to an abasic site
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 / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / 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 / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_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)69,7168
Polymers69,3693
Non-polymers3475
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-17 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.460, 109.460, 90.427
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-62-

HOH

21A-876-

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*(DOC))-3')


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

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Non-polymers , 4 types, 355 molecules

#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M TRIS HCl pH 7.5, 0.2 M Magnesium Formate, 12% 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: Feb 17, 2011
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: 1.95→50 Å / Num. all: 451750 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.11 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.29
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.97 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.27 / Num. unique all: 13522 / % possible all: 93.6

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Processing

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

3lwl


Resolution: 1.95→47.398 Å / SU ML: 0.58 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 4474 5.07 %Random
Rwork0.1932 ---
obs0.1951 88190 99.76 %-
all-88190 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.854 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.4328 Å2-0 Å2-0 Å2
2--3.4328 Å2-0 Å2
3----6.8655 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 541 22 350 4976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024796
X-RAY DIFFRACTIONf_angle_d0.7396609
X-RAY DIFFRACTIONf_dihedral_angle_d15.7211841
X-RAY DIFFRACTIONf_chiral_restr0.049730
X-RAY DIFFRACTIONf_plane_restr0.003770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-1.97220.34831670.31522658X-RAY DIFFRACTION94
1.9722-1.99540.331490.30092800X-RAY DIFFRACTION100
1.9954-2.01980.32661710.28212753X-RAY DIFFRACTION100
2.0198-2.04530.28351550.26592757X-RAY DIFFRACTION100
2.0453-2.07220.30121550.26442804X-RAY DIFFRACTION100
2.0722-2.10060.27891320.24372840X-RAY DIFFRACTION100
2.1006-2.13060.32471370.23412778X-RAY DIFFRACTION100
2.1306-2.16240.29751180.21942832X-RAY DIFFRACTION100
2.1624-2.19620.24381560.22542782X-RAY DIFFRACTION100
2.1962-2.23220.30581260.21712852X-RAY DIFFRACTION100
2.2322-2.27070.28081370.21052776X-RAY DIFFRACTION100
2.2707-2.3120.22411550.19492765X-RAY DIFFRACTION100
2.312-2.35650.22681310.20422840X-RAY DIFFRACTION100
2.3565-2.40460.30361160.20992867X-RAY DIFFRACTION100
2.4046-2.45690.25411400.21492761X-RAY DIFFRACTION100
2.4569-2.5140.26731380.20822808X-RAY DIFFRACTION100
2.514-2.57690.24961740.21242791X-RAY DIFFRACTION100
2.5769-2.64660.30081580.21052774X-RAY DIFFRACTION100
2.6466-2.72440.25711530.222808X-RAY DIFFRACTION100
2.7244-2.81230.24061500.20522791X-RAY DIFFRACTION100
2.8123-2.91280.25221530.20542766X-RAY DIFFRACTION100
2.9128-3.02950.20251560.19542804X-RAY DIFFRACTION100
3.0295-3.16730.23671300.19842810X-RAY DIFFRACTION100
3.1673-3.33430.2491760.1862797X-RAY DIFFRACTION100
3.3343-3.54310.18551320.17512783X-RAY DIFFRACTION100
3.5431-3.81650.21051830.17122760X-RAY DIFFRACTION100
3.8165-4.20040.17111780.15462768X-RAY DIFFRACTION100
4.2004-4.80770.20631390.14232810X-RAY DIFFRACTION100
4.8077-6.05520.20611460.16812796X-RAY DIFFRACTION100
6.0552-47.41160.1991630.17822785X-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)
12.70320.6955-0.00241.63380.06910.77150.1379-0.0416-0.7125-0.1175-0.0274-0.35740.33220.00270.02850.139-0.15360.0280.27850.04330.291639.6974-42.11-18.165
20.92740.7825-0.22430.9433-0.43941.433-0.00670.00770.27580.36890.03020.0982-0.5092-0.2512-0.01080.1713-0.0410.11620.15360.06310.10332.1407-12.5409-2.153
32.2698-0.32580.12572.6661-1.28071.6690.0202-0.49670.42841.5942-0.07550.4285-0.8934-0.36530.00231.35650.26890.04341.13520.03720.64596.6422-15.7026-1.3002
40.50330.12050.00950.6311-0.29471.6327-0.13560.0042-0.0994-0.10520.26570.232-0.0149-0.5636-0.12570.0899-0.17420.08470.48280.18280.008819.1532-26.1422-15.1487
51.9530.84070.0210.5258-0.27960.67550.10340.4559-0.3440.1042-0.2735-0.21590.07440.5760.0610.21520.08440.01270.3870.06070.253636.883-23.0374.1696
63.2281.46150.68872.680.65643.7339-0.3944-0.14740.12290.1390.26040.0666-0.2234-0.41130.10840.18610.0289-0.00020.31560.06590.137734.1732-22.87594.0516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 295:446)
2X-RAY DIFFRACTION2(chain A and resid 447:633)
3X-RAY DIFFRACTION3(chain A and resid 634:698)
4X-RAY DIFFRACTION4(chain A and resid 699:832)
5X-RAY DIFFRACTION5(chain B)
6X-RAY DIFFRACTION6(chain C)

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