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- PDB-3ojs: Snapshots of the large fragment of DNA polymerase I from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 3ojs
TitleSnapshots of the large fragment of DNA polymerase I from Thermus Aquaticus processing C5 modified thymidines
Components
  • DNA (5'-D(*AP*AP*AP*AP*GP*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*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTransferase/DNA / DNA polymerase / C5 modified nucleotide analogs / binding pocket / denron-labeled triphosphate / 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 / TRIETHYLENE GLYCOL / Chem-XJS / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase.
Authors: Obeid, S. / Baccaro, A. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionAug 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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.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_conn.ptnr2_label_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: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
C: DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,11121
Polymers69,5033
Non-polymers2,60818
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.829, 107.829, 90.197
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-840-

ACT

21A-840-

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: unp residues 292-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / 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*(DOC))-3')


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide
#3: DNA chain DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide

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Non-polymers , 6 types, 349 molecules

#4: Chemical ChemComp-XJS / 2'-deoxy-5-[9-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-18-ethyl-5,8,14,17-tetraoxo-4,9,13,18-tetraazaicos-1-yn-1-yl]uridine 5'-(tetrahydrogen triphosphate)


Mass: 1044.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H63N8O20P3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Na cacodylate ph 6.5, 0.2M NH4OAc, 0.01M Mg(OAc)2, 26% PEG 8000, 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: May 20, 2010
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 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: 1.9→50 Å / Num. obs: 47553 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 40.024 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 14.71
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 1.58 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.6.4_486phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M8R

3m8r


Resolution: 1.9→46.691 Å / SU ML: 0.22 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 2401 5.05 %random
Rwork0.1634 ---
obs0.1659 47553 99.03 %-
all-47553 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.124 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.3171 Å20 Å2-0 Å2
2--1.3171 Å2-0 Å2
3----2.6343 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 569 148 331 5334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065161
X-RAY DIFFRACTIONf_angle_d1.127080
X-RAY DIFFRACTIONf_dihedral_angle_d17.6362040
X-RAY DIFFRACTIONf_chiral_restr0.061762
X-RAY DIFFRACTIONf_plane_restr0.01818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93880.28231230.25782333X-RAY DIFFRACTION89
1.9388-1.98090.33891490.24652600X-RAY DIFFRACTION98
1.9809-2.0270.26421500.22792611X-RAY DIFFRACTION99
2.027-2.07770.23551450.19262657X-RAY DIFFRACTION99
2.0777-2.13390.26271260.19072643X-RAY DIFFRACTION100
2.1339-2.19670.22991300.18342670X-RAY DIFFRACTION100
2.1967-2.26760.26761320.17582661X-RAY DIFFRACTION100
2.2676-2.34860.2331310.1612657X-RAY DIFFRACTION100
2.3486-2.44270.2281250.16052675X-RAY DIFFRACTION100
2.4427-2.55380.23051470.16092674X-RAY DIFFRACTION100
2.5538-2.68840.23631490.16432638X-RAY DIFFRACTION100
2.6884-2.85690.20041430.16562679X-RAY DIFFRACTION100
2.8569-3.07740.22861320.17052696X-RAY DIFFRACTION100
3.0774-3.3870.18891550.1572693X-RAY DIFFRACTION100
3.387-3.87690.1841580.14232695X-RAY DIFFRACTION100
3.8769-4.88370.17461450.12812737X-RAY DIFFRACTION100
4.8837-46.70540.20821610.17452833X-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)
10.35140.2176-0.00560.465-0.00690.83560.00830.0025-0.0396-0.07450.0043-0.09480.047-0.0506-0.01450.1791-0.03120.00890.16010.01390.181235.7495-25.5804-9.0924
21.4708-0.609-0.66471.8538-1.33621.9377-0.2539-0.32630.00720.72680.64150.2248-0.8886-0.5873-0.3490.60780.36170.08780.64220.08990.2719.0381-11.7539-3.204
30.1274-0.23480.40470.6309-0.47931.528-0.06040.0275-0.014-0.0960.20180.1538-0.0251-0.4964-0.14660.1673-0.0298-0.00370.27250.04530.18118.6428-25.7855-14.8447
40.03990.0039-0.29012.0293-1.49813.0466-0.0541-0.0153-0.04050.1271-0.1202-0.0996-0.17570.3460.14590.1162-0.0241-0.01490.19420.01960.253336.5261-22.71894.2044
50.27310.4310.0310.7187-0.1771.0557-0.1501-0.0492-0.15010.00760.1806-0.0866-0.0184-0.1328-0.02950.16460.0396-0.0230.24520.01990.180134.0305-23.66715.5616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 295:627)
2X-RAY DIFFRACTION2(chain A and resid 628:697)
3X-RAY DIFFRACTION3(chain A and resid 698:832)
4X-RAY DIFFRACTION4(chain B and resid 101:112)
5X-RAY DIFFRACTION5(chain C and resid 203:216)

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