+Open data
-Basic information
Entry | Database: PDB / ID: 3g00 | ||||||
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Title | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | ||||||
Components |
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Keywords | HYDROLASE/DNA / protein-DNA complex / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-deoxyuridine endonuclease / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / endonuclease activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Lakomek, K. / Dickmanns, A. / Ficner, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA Authors: Lakomek, K. / Dickmanns, A. / Ciirdaeva, E. / Schomacher, L. / Ficner, R. #1: Journal: Nucleic Acids Res. / Year: 2006 Title: The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease Authors: Georg, J. / Schomacher, L. / Chong, J.P.J. / Majernik, A.I. / Raabe, M. / Urlaub, H. / Muller, S. / Ciirdaeva, E. / Kramer, W. / Fritz, H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g00.cif.gz | 150 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g00.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 3g00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g00_validation.pdf.gz | 478.2 KB | Display | wwPDB validaton report |
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Full document | 3g00_full_validation.pdf.gz | 484.8 KB | Display | |
Data in XML | 3g00_validation.xml.gz | 29 KB | Display | |
Data in CIF | 3g00_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/3g00 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/3g00 | HTTPS FTP |
-Related structure data
Related structure data | 3fziSC 3g0aC 3g0rC 3g1kC 3g2cC 3g2dC 3g38C 3g3cC 3g3yC 3g4tC 3g8vC 3g91C 3ga6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31429.666 Da / Num. of mol.: 2 / Mutation: T2A, D151N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (D151N) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O26314, exodeoxyribonuclease III |
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-DNA chain , 2 types, 2 molecules HI
#2: DNA chain | Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 2716.784 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 668 molecules
#4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: reservoir: 30% MPD, 40mM MgCl2, 50mM KH2PO4/K2HPO4 pH 7.0; protein solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91838 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91838 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.74→17 Å / Num. obs: 65383 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.283 Å2 / Rmerge(I) obs: 0.033 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FZI Resolution: 1.74→17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.868 / SU B: 2.422 / SU ML: 0.079 / SU R Cruickshank DPI: 0.11 / SU Rfree: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.2 Å2 / Biso mean: 24.824 Å2 / Biso min: 8.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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