+Open data
-Basic information
Entry | Database: PDB / ID: 3vup | ||||||
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Title | Beta-1,4-mannanase from the common sea hare Aplysia kurodai | ||||||
Components | Beta-1,4-mannanase | ||||||
Keywords | HYDROLASE / Tim Barrel / Beta-1 / 4-mannanase / mannan / digestive fluid | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Aplysia kurodai (Kuroda's sea hare) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Mizutani, K. / Tsuchiya, S. / Toyoda, M. / Nanbu, Y. / Tominaga, K. / Yuasa, K. / Takahashi, N. / Tsuji, A. / Mikami, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of beta-1,4-mannanase from the common sea hare Aplysia kurodai at 1.05 A resolution. Authors: Mizutani, K. / Tsuchiya, S. / Toyoda, M. / Nanbu, Y. / Tominaga, K. / Yuasa, K. / Takahashi, N. / Tsuji, A. / Mikami, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vup.cif.gz | 347.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vup.ent.gz | 294.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/3vup ftp://data.pdbj.org/pub/pdb/validation_reports/vu/3vup | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40014.895 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-369 / Source method: isolated from a natural source / Source: (natural) Aplysia kurodai (Kuroda's sea hare) / References: UniProt: E5RSM0 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.1M sodium sulfate, 100mM Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 31, 2010 |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. all: 296609 / Num. obs: 292160 / % possible obs: 98.5 % / Observed criterion σ(I): 25.8 |
Reflection shell | Resolution: 1.05→1.07 Å / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→24.95 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 12.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.791 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.05→24.95 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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