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Yorodumi- PDB-3wa6: Crystal structure of tannase from Lactobacillus plantarum in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wa6 | ||||||
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Title | Crystal structure of tannase from Lactobacillus plantarum in the orthorhombic crystal | ||||||
Components | tannase | ||||||
Keywords | HYDROLASE / alpha/beta-hydrolase | ||||||
Function / homology | : / : / BD-FAE / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Tannase Function and homology information | ||||||
Biological species | Lactobacillus plantarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Matoba, Y. / Tanaka, N. / Sugiyama, M. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Crystallographic and mutational analyses of tannase from Lactobacillus plantarum Authors: Matoba, Y. / Tanaka, N. / Noda, M. / Higashikawa, F. / Kumagai, T. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wa6.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wa6.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wa6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wa6_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 3wa6_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 3wa6_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3wa6_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wa6 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wa6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 51835.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: SN35N / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3Y018*PLUS, EC: 3.1.1.20 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.66 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG8000, sodium acetate, ammonium sulfate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 22, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 41361 / Num. obs: 41361 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3887 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→23.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3617886.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.4802 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→23.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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