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

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Basic information

Entry
Database: PDB / ID: 3syz
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase
Components
  • (5'-D(*AP*AP*AP*(BMN)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 / artificial base / 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 / Difference Fourier Techniques / Resolution: 1.952 Å
AuthorsBetz, K. / Diederichs, K. / Marx, A.
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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _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*(DOC))-3')
C: (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,77121
Polymers69,5263
Non-polymers1,24618
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-30 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.529, 108.529, 90.524
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-850-

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


Mass: 4971.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 4 types, 342 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11% PEG 8000, 0.2M MgFormate, 0.1M Tris, 20mM MgCl2, 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: 1.0015 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 1.95→47 Å / Num. all: 45113 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Net I/σ(I): 11.23
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.21 / % possible all: 98.6

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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: 1.952→46.543 Å / SU ML: 0.47 / Isotropic thermal model: isotropic and tls / σ(F): 1.44 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 4367 5.05 %
Rwork0.1602 --
obs0.1623 86484 99.7 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.198 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9774 Å2-0 Å2-0 Å2
2--0.9774 Å2-0 Å2
3----1.9548 Å2
Refinement stepCycle: LAST / Resolution: 1.952→46.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 571 80 324 5241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065142
X-RAY DIFFRACTIONf_angle_d1.0777068
X-RAY DIFFRACTIONf_dihedral_angle_d16.7762008
X-RAY DIFFRACTIONf_chiral_restr0.061772
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9518-1.9740.27971440.25992529X-RAY DIFFRACTION91
1.974-1.99720.23941480.22922722X-RAY DIFFRACTION100
1.9972-2.02160.26861670.21652749X-RAY DIFFRACTION100
2.0216-2.04720.23421360.21472815X-RAY DIFFRACTION100
2.0472-2.07410.29581420.2092656X-RAY DIFFRACTION100
2.0741-2.10250.24151470.19612746X-RAY DIFFRACTION100
2.1025-2.13250.24991350.19422771X-RAY DIFFRACTION100
2.1325-2.16440.2271230.18152737X-RAY DIFFRACTION100
2.1644-2.19820.25641410.18562786X-RAY DIFFRACTION100
2.1982-2.23420.22621150.17412741X-RAY DIFFRACTION100
2.2342-2.27280.23861510.16682770X-RAY DIFFRACTION100
2.2728-2.31410.20561470.172736X-RAY DIFFRACTION100
2.3141-2.35860.22111260.17622774X-RAY DIFFRACTION100
2.3586-2.40670.27381170.17322727X-RAY DIFFRACTION100
2.4067-2.45910.25021350.16832768X-RAY DIFFRACTION100
2.4591-2.51630.23651650.16662763X-RAY DIFFRACTION100
2.5163-2.57920.23421390.16792744X-RAY DIFFRACTION100
2.5792-2.64890.25351630.16692726X-RAY DIFFRACTION100
2.6489-2.72690.23411550.16052696X-RAY DIFFRACTION100
2.7269-2.81490.22951420.16012786X-RAY DIFFRACTION100
2.8149-2.91550.21041550.14962684X-RAY DIFFRACTION100
2.9155-3.03220.1741460.15042779X-RAY DIFFRACTION100
3.0322-3.17010.15921310.1442760X-RAY DIFFRACTION100
3.1701-3.33720.17371650.14152704X-RAY DIFFRACTION100
3.3372-3.54620.16391490.13292772X-RAY DIFFRACTION100
3.5462-3.81990.17011680.13592729X-RAY DIFFRACTION100
3.8199-4.20410.16671770.13892699X-RAY DIFFRACTION100
4.2041-4.81190.16241310.12572759X-RAY DIFFRACTION100
4.8119-6.06040.22481460.17222758X-RAY DIFFRACTION100
6.0604-46.5560.18831610.18412731X-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)
11.6084-0.0305-0.32792.4588-0.17361.0012-0.00110.0086-0.2196-0.1163-0.0336-0.27490.16910.12210.04020.1846-0.00340.0030.1783-0.00460.165239.8577-41.6799-18.3388
20.54860.58620.34520.97620.33291.2566-0.0144-0.08540.19270.0695-0.01040.1154-0.1605-0.03630.03330.1942-0.00080.02830.1898-0.0060.223231.194-12.7109-2.1252
35.42870.7694-2.19676.35210.76976.87410.3139-0.9881.51871.14580.11470.6407-1.6821-0.6189-0.39280.74530.12230.22170.7117-0.11540.83646.3466-12.3869-0.4881
42.00020.4306-0.3861.702-1.06732.47270.0108-0.07230.01610.03670.1280.2226-0.0856-0.2767-0.11110.1643-0.0074-0.00030.19250.00470.165418.2352-25.8501-14.4557
53.7271.1580.21152.5779-0.5521.41570.06070.2028-0.53760.5367-0.2643-0.0391-0.14120.62880.1220.25210.0388-0.00290.3-0.01150.25136.5971-22.9074.426
61.55771.4725-1.13153.85670.99392.5915-0.2905-0.02650.02140.14670.11630.11440.01170.01130.21130.19620.0151-0.01210.19710.00590.142333.437-22.90644.3367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 293:450)
2X-RAY DIFFRACTION2(chain A and resid 451:635)
3X-RAY DIFFRACTION3(chain A and resid 636:693)
4X-RAY DIFFRACTION4(chain A and resid 694:832)
5X-RAY DIFFRACTION5(chain B and resid 101:112)
6X-RAY DIFFRACTION6(chain C and resid 202:216)

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