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- PDB-3lwm: Structure of the large fragment of thermus aquaticus DNA polymera... -

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Basic information

Entry
Database: PDB / ID: 3lwm
TitleStructure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA replication / DNA polymerases / DNA-binding / DNA-directed DNA polymerase / amino acid-templating mechanism / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex / blunt-ended DNA / template-independent DNA synthesis / terminal deoxynucleotidyl transferase / template-independent nucleotide addition
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: 2.186 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 / 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(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,53718
Polymers68,2493
Non-polymers1,28815
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-12 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.592, 109.592, 91.037
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-3-

ACT

21A-3-

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: 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(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 3670.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA

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Non-polymers , 6 types, 169 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 154 / 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: 46.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.05M TRIS HCl, pH 8, 0.2M ammonium chloride, 0.01M calcium chloride and 35% PEG 4000, 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 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: 2.186→50 Å / Num. obs: 32557 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.61 % / Biso Wilson estimate: 42.37 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.96
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 8.08 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.53 / Num. unique all: 4863 / % possible all: 93.4

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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: 2.186→47.455 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.843 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1639 5.03 %RANDOM
Rwork0.1834 ---
all0.1857 32553 --
obs0.1857 32553 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.855 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 182.08 Å2 / Biso mean: 52.4 Å2 / Biso min: 14.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.176 Å20 Å2-0 Å2
2--2.176 Å20 Å2
3----4.352 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.186→47.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 485 80 154 4995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064986
X-RAY DIFFRACTIONf_angle_d0.8516835
X-RAY DIFFRACTIONf_dihedral_angle_d17.1481917
X-RAY DIFFRACTIONf_chiral_restr0.053745
X-RAY DIFFRACTIONf_plane_restr0.003806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1859-2.25020.3083990.26082161X-RAY DIFFRACTION83
2.2502-2.32290.31331400.24242517X-RAY DIFFRACTION98
2.3229-2.40590.29951170.22652600X-RAY DIFFRACTION100
2.4059-2.50220.27971240.21242648X-RAY DIFFRACTION100
2.5022-2.61610.27451440.20352555X-RAY DIFFRACTION100
2.6161-2.7540.25461490.19912585X-RAY DIFFRACTION100
2.754-2.92650.2461360.1972605X-RAY DIFFRACTION100
2.9265-3.15240.25151320.1842607X-RAY DIFFRACTION100
3.1524-3.46960.21531450.17742618X-RAY DIFFRACTION100
3.4696-3.97140.2031570.16072618X-RAY DIFFRACTION100
3.9714-5.00270.19691400.15212660X-RAY DIFFRACTION100
5.0027-47.46590.18471560.16212740X-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)
10.71560.5479-0.23931.031-0.54471.4843-0.0890.1275-0.1115-0.04370.0589-0.2013-0.1513-0.19750.00190.1569-0.07660.04070.156-0.01030.13936.1337-26.1597-9.1061
23.4787-1.01480.02213.459-0.31110.0327-0.1548-0.37970.17560.7460.4264-0.0369-0.9634-0.5499-0.32720.58850.32490.06020.88230.0150.17057.035-13.4529-3.3222
30.86260.09730.33350.66060.14591.2148-0.20.2479-0.0482-0.24650.2650.0372-0.1045-0.6336-0.09110.1281-0.08110.00340.41710.02630.050819.036-26.2055-14.8654
42.5249-0.68451.15782.4766-2.46762.6790.03420.3413-0.05040.2826-0.2943-0.2316-0.39270.20790.24590.1621-0.0092-0.0240.1830.01910.160937.1607-23.21864.2743
52.6091.30181.3381.39290.01262.6524-0.3489-0.0128-0.34510.02120.3084-0.2301-0.19530.13770.02440.15460.0565-0.040.2480.01510.185138.5396-24.26595.6104
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 204:216)C204 - 216

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