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Yorodumi- PDB-3g38: The catalytically inactive mutant Mth0212 (D151N) in complex with... -
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-Basic information
Entry | Database: PDB / ID: 3g38 | ||||||
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Title | The catalytically inactive mutant Mth0212 (D151N) in complex with an 8 bp dsDNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / protein-DNA complex / 3'- phosphate moiety bound / 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 / molecular replacement / Resolution: 3.04 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 | 3g38.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g38.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g38_validation.pdf.gz | 456.4 KB | Display | wwPDB validaton report |
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Full document | 3g38_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | 3g38_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3g38_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/3g38 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g38 | HTTPS FTP |
-Related structure data
Related structure data | 3fziSC 3g00C 3g0aC 3g0rC 3g1kC 3g2cC 3g2dC 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
#1: Protein | Mass: 31429.666 Da / Num. of mol.: 1 / 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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#2: DNA chain | Mass: 3021.964 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: DNA chain | Mass: 2741.800 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.55 Å3/Da / Density % sol: 51.75 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: reservoir: 5% (w/v) PEG 4000, 50mM KCl, 100mM MES pH 5.6, 10mM MgCl2; complex solution: 230mM NaCl, 8mM HEPES-KOH pH 7.6, 2mM MgCl2, 3mM DTT, 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 17, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8015 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.74→36.424 Å / Num. obs: 10553 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 5.881 / Num. measured all: 80599 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDN ENTRY 3FZI Resolution: 3.04→34.13 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.779 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.235 / Occupancy max: 1 / Occupancy min: 0.99 / FOM work R set: 0.711 / SU B: 30.97 / SU ML: 0.55 / SU Rfree: 0.594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.594 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The DNA conformation significantly deviates from ideal geometry due to the binding to the protein molecule
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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: 93.28 Å2 / Biso mean: 37.113 Å2 / Biso min: 18.88 Å2
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Refinement step | Cycle: LAST / Resolution: 3.04→34.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.04→3.119 Å / Total num. of bins used: 20
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