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- PDB-3sz2: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 3sz2
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dG as templating nucleobase
Components
  • (5'-D(*AP*AP*AP*GP*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 / binary complex / 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
FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Techniques / Resolution: 2.15 Å
AuthorsBetz, K. / Marx, A. / Diederichs, K.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Dwyer, T.J. / Ordoukhanian, P. / Romesberg, F.E. / Marx, A.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Sep 12, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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')
D: (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,91111
Polymers69,5193
Non-polymers3938
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-18 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.398, 108.398, 89.752
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-222-

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: pol I, pol1, polA / 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 BD

#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 / Source method: obtained synthetically / Details: DNA synthesizer
#3: DNA chain (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4924.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 4 types, 303 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 8000, 0.2M MgFormate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.23 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2.15→46.9 Å / Num. all: 33563 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Net I/σ(I): 14.77
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 11 % / Num. unique all: 5352 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: Difference Fourier Techniques
Starting model: PDB ENTRY 4KTQ

4ktq


Resolution: 2.15→46.938 Å / SU ML: 0.64 / Isotropic thermal model: isotropic and tls / σ(F): 1.3 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 3261 5.08 %random
Rwork0.1897 ---
obs0.1921 64185 99.99 %-
all-64185 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.846 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9046 Å2-0 Å2-0 Å2
2--2.9046 Å2-0 Å2
3----5.8092 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 510 25 295 5012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034897
X-RAY DIFFRACTIONf_angle_d0.7586736
X-RAY DIFFRACTIONf_dihedral_angle_d16.3121887
X-RAY DIFFRACTIONf_chiral_restr0.044745
X-RAY DIFFRACTIONf_plane_restr0.003791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18210.32641530.30322667X-RAY DIFFRACTION100
2.1821-2.21620.34341110.29312662X-RAY DIFFRACTION100
2.2162-2.25250.30381370.26562642X-RAY DIFFRACTION100
2.2525-2.29140.30321410.25912616X-RAY DIFFRACTION100
2.2914-2.3330.29211270.25512670X-RAY DIFFRACTION100
2.333-2.37790.34721130.24892678X-RAY DIFFRACTION100
2.3779-2.42640.34651270.24822686X-RAY DIFFRACTION100
2.4264-2.47920.29611340.23832651X-RAY DIFFRACTION100
2.4792-2.53690.29911570.23562626X-RAY DIFFRACTION100
2.5369-2.60030.32491470.21952668X-RAY DIFFRACTION100
2.6003-2.67060.33891490.22882626X-RAY DIFFRACTION100
2.6706-2.74920.25821300.20982662X-RAY DIFFRACTION100
2.7492-2.83790.26471600.20442633X-RAY DIFFRACTION100
2.8379-2.93930.25571570.20462635X-RAY DIFFRACTION100
2.9393-3.0570.26861140.20362664X-RAY DIFFRACTION100
3.057-3.19610.22421540.18542685X-RAY DIFFRACTION100
3.1961-3.36450.19581400.16342603X-RAY DIFFRACTION100
3.3645-3.57530.18831450.15292653X-RAY DIFFRACTION100
3.5753-3.85120.21081730.15562619X-RAY DIFFRACTION100
3.8512-4.23850.16331700.13782612X-RAY DIFFRACTION100
4.2385-4.85130.21981210.13392677X-RAY DIFFRACTION100
4.8513-6.110.19191470.17112647X-RAY DIFFRACTION100
6.11-46.94890.21811540.17822642X-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)
11.6181-0.07860.01782.3469-0.02981.36520.01620.0758-0.3285-0.2777-0.0554-0.30440.34950.07120.03770.2601-0.08440.05020.1809-0.02670.218139.3133-41.4881-18.3571
21.33581.0885-0.06791.2412-0.07491.67670.0727-0.02210.18120.2187-0.04150.0799-0.3915-0.2504-0.00370.2840.00860.03880.19330.02920.220731.7488-12.2738-1.6518
33.327-1.19890.03571.39151.22472.8066-0.5914-0.48190.6570.62850.19490.3311-1.96-0.94240.19271.11320.5154-0.07030.9248-0.04120.64186.7291-13.9529-0.4545
41.11040.2155-0.01610.9628-0.28572.4157-0.20980.04830.079-0.35570.2220.2343-0.362-0.8904-0.1051-0.0316-0.13830.01590.31290.06790.109218.7561-25.8786-14.7325
52.57450.5261-0.41130.1494-0.06610.08690.12990.1471-0.57450.355-0.4045-0.19890.09810.73180.14330.27690.0493-0.0720.38570.09720.365937.6138-23.29065.1568
61.39452.33120.42223.97040.24154.1915-0.1595-0.24470.02480.29220.0574-0.16140.0350.08760.19520.23420.0693-0.01350.2735-0.00150.169735.9345-23.70695.3434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 293:450)
2X-RAY DIFFRACTION2(chain A and resid 451:634)
3X-RAY DIFFRACTION3(chain A and resid 635:697)
4X-RAY DIFFRACTION4(chain A and resid 698:832)
5X-RAY DIFFRACTION5(chain B and resid 101:111)
6X-RAY DIFFRACTION6(chain D and resid 203:216)

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