+Open data
-Basic information
Entry | Database: PDB / ID: 3g91 | ||||||
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Title | 1.2 Angstrom structure of the exonuclease III homologue Mth0212 | ||||||
Components | Exodeoxyribonuclease | ||||||
Keywords | HYDROLASE / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-desoxyuridine endonuclease | ||||||
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: 1.23 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 | 3g91.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g91.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g91_validation.pdf.gz | 461.9 KB | Display | wwPDB validaton report |
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Full document | 3g91_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 3g91_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 3g91_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g91 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g91 | HTTPS FTP |
-Related structure data
Related structure data | 3fziSC 3g00C 3g0aC 3g0rC 3g1kC 3g2cC 3g2dC 3g38C 3g3cC 3g3yC 3g4tC 3g8vC 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, 1 molecules A
#1: Protein | Mass: 31372.549 Da / Num. of mol.: 1 / Mutation: T2A, K116A 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 (K116A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_UX / References: UniProt: O26314, exodeoxyribonuclease III |
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-Non-polymers , 6 types, 438 molecules
#2: Chemical | ChemComp-PO4 / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-PG4 / |
#7: 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: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: reservoir solution: 20% (v/v) MPD, 40mM MgAc, 50mM sodium cacodylate pH 6.0; protein solution: 180mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→18 Å / Num. obs: 73200 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 15.044 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.23→1.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 9 / Num. measured obs: 23038 / Num. unique all: 6790 / Num. unique obs: 6297 / % possible all: 92.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FZI Resolution: 1.23→9.99 Å / Num. parameters: 24979 / Num. restraintsaints: 32073 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH AND HUBER / Details: anisotropic factor was used in refinement
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Displacement parameters | Biso max: 153.29 Å2 / Biso mean: 20.046 Å2 / Biso min: 3.27 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2606.71 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→9.99 Å
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Refine LS restraints |
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