+Open data
-Basic information
Entry | Database: PDB / ID: 3wyd | ||||||
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Title | C-terminal esterase domain of LC-Est1 | ||||||
Components | LC-Est1C | ||||||
Keywords | HYDROLASE / Leaf-branch compost / Metagenome / Alpha/beta hydrolase fold / Esterase | ||||||
Function / homology | Function and homology information methyl indole-3-acetate esterase activity / carboxylesterase / serine-type peptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | uncultured organism (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.53 Å | ||||||
Authors | Okano, H. / Hong, X. / Angkawidjaja, C. / Kanaya, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Structural and biochemical characterization of a metagenome-derived esterase with a long N-terminal extension. Authors: Okano, H. / Hong, X. / Kanaya, E. / Angkawidjaja, C. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wyd.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wyd.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/3wyd ftp://data.pdbj.org/pub/pdb/validation_reports/wy/3wyd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25135.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured organism (environmental samples) Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A6YVN5*PLUS, carboxylesterase #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium chloride, 0.1M BIS-TRIS, 25% PEG3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.53→78.14 Å / Num. obs: 60179 / % possible obs: 98.5 % / Observed criterion σ(I): 5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 14.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.53→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.281 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.087 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.156 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→50 Å
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Refine LS restraints |
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