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- PDB-3lwl: Structure of Klenow fragment of Taq polymerase in complex with an... -

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Basic information

Entry
Database: PDB / ID: 3lwl
TitleStructure of Klenow fragment of Taq polymerase in complex with an abasic site
Components
  • DNA (5'-D(*AP*AP*AP*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA replication / DNA repair / DNA polymerases / Abasic sites / Translesion synthesis / DNA damage / DNA-binding / DNA-directed DNA polymerase / amino acid-templating mechanism / 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
ACETATE ION / 2',3'-dideoxyadenosine triphosphate / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S.
CitationJournal: Embo J. / Year: 2010
Title: Replication through an abasic DNA lesion: structural basis for adenine selectivity
Authors: Obeid, S. / Blatter, N. / Kranaster, R. / Schnur, A. / Diederichs, K. / Welte, W. / Marx, A.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_special_symmetry / 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.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.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.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 (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
C: DNA (5'-D(*AP*AP*AP*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,90021
Polymers69,3683
Non-polymers1,53118
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-16 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.228, 110.228, 91.265
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-2-

ACT

21A-2-

ACT

31A-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, UNP residues 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: 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 DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')


Mass: 3641.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain DNA (5'-D(*AP*AP*AP*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4790.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA

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Non-polymers , 6 types, 179 molecules

#4: Chemical ChemComp-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M sodium cacodylate, 0.2M ammonium acetate, 0.01M magnesium acetate, 30% PEG 8000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2009
Details: vertically collimating mirror (M1, focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry, and a toroidal mirror (M2)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 30775 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.78 % / Biso Wilson estimate: 43.283 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 16.11
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 9.94 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.48 / Num. unique all: 4843 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6_289)model building
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.6_289phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KTQ

3ktq


Resolution: 2.25→47.73 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.836 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1560 5.08 %RANDOM
Rwork0.1883 ---
all0.1906 30730 --
obs0.1906 30730 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.922 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 291.28 Å2 / Biso mean: 52.624 Å2 / Biso min: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.467 Å20 Å20 Å2
2---0.467 Å2-0 Å2
3---0.933 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.25→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 520 96 161 5013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164992
X-RAY DIFFRACTIONf_angle_d0.9296841
X-RAY DIFFRACTIONf_dihedral_angle_d18.4691913
X-RAY DIFFRACTIONf_chiral_restr0.056745
X-RAY DIFFRACTIONf_plane_restr0.003797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2502-2.32280.28341370.24992578X-RAY DIFFRACTION99
2.3228-2.40580.27111210.23112665X-RAY DIFFRACTION100
2.4058-2.50210.27091270.2292623X-RAY DIFFRACTION100
2.5021-2.6160.27661470.22762620X-RAY DIFFRACTION100
2.616-2.75390.28371490.22242626X-RAY DIFFRACTION100
2.7539-2.92640.26541390.21772624X-RAY DIFFRACTION100
2.9264-3.15230.28131360.20162669X-RAY DIFFRACTION100
3.1523-3.46950.23611500.18952643X-RAY DIFFRACTION100
3.4695-3.97130.191530.1572653X-RAY DIFFRACTION100
3.9713-5.00260.18061410.1492685X-RAY DIFFRACTION100
5.0026-47.74080.2131600.16852784X-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)
11.74321.0417-0.20181.0079-0.48451.684-0.16680.2947-0.3503-0.0840.1199-0.3073-0.2679-0.21740.00190.0785-0.07570.04980.1502-0.03140.148436.1207-26.1347-9.2346
25.8724-1.64370.53494.3514-0.7910.1501-0.0849-0.31730.23470.94390.61370.1279-1.0082-0.7969-0.34770.73550.5210.04281.13480.00560.27086.4281-14.0125-3.3679
31.01740.37040.36170.76960.05072.4774-0.34140.4929-0.0986-0.28240.4156-0.0808-0.177-1.0274-0.16320.1238-0.08670.03270.56290.03720.010518.9929-26.2947-15.0833
41.35560.44480.54192.7281-2.62114.7691-0.10110.3964-0.10640.256-0.3546-0.4148-0.37860.29230.42910.09150.038-0.00630.26170.05960.172537.3551-23.52194.2489
51.10210.8486-1.0360.8395-0.41181.6975-0.27370.0592-0.31570.12480.1936-0.21420.019-0.02370.02750.15730.0572-0.06870.21860.06410.19535.6396-24.47445.9074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 295:627)A295 - 627
2X-RAY DIFFRACTION2(chain A and resid 628:697)A628 - 697
3X-RAY DIFFRACTION3(chain A and resid 698:832)A698 - 832
4X-RAY DIFFRACTION4(chain B and resid 101:112)B101 - 112
5X-RAY DIFFRACTION5(chain C and resid 203:216)C203 - 216

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