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Yorodumi- PDB-3g8v: The rationally designed catalytically inactive mutant Mth0212(D151N) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g8v | ||||||
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Title | The rationally designed catalytically inactive mutant Mth0212(D151N) | ||||||
Components | Exodeoxyribonuclease | ||||||
Keywords | HYDROLASE / alpha/beta-sandwich / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-desoxyuridine endonuclease / rationally designed catalytically inactive mutant | ||||||
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: 2.4 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 | 3g8v.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g8v.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 3g8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g8v_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 3g8v_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 3g8v_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3g8v_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/3g8v ftp://data.pdbj.org/pub/pdb/validation_reports/g8/3g8v | HTTPS FTP |
-Related structure data
Related structure data | 3fziSC 3g00C 3g0aC 3g0rC 3g1kC 3g2cC 3g2dC 3g38C 3g3cC 3g3yC 3g4tC 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
#1: Protein | Mass: 31429.666 Da / Num. of mol.: 1 / Mutation: T2A, D151N Source method: isolated from a genetically manipulated source Details: strain used for expression lacks the gene ung coding for a uracil DNA glycosylase 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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#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: reservoir solution: 15 % (w/v) PEG 3350, 15mM sodium cacodylate pH 6.5, 25mM MnCl2; protein solution: 120mM NaCl, 2mM DTT, 8mM HEPES-NaOH pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30.39 Å / Num. obs: 12026 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FZI Resolution: 2.4→29.56 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.216 / Occupancy max: 1 / Occupancy min: 0.99 / FOM work R set: 0.764 / SU B: 9.361 / SU ML: 0.229 / SU R Cruickshank DPI: 0.526 / SU Rfree: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.304 / 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: 75.77 Å2 / Biso mean: 39.781 Å2 / Biso min: 22.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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