+Open data
-Basic information
Entry | Database: PDB / ID: 3p5v | ||||||
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Title | Actinidin from Actinidia arguta planch (Sarusashi) | ||||||
Components | ActinidinActinidain | ||||||
Keywords | HYDROLASE / SAD / Cysteine proteinases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Actinidia arguta (plant) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.9 Å | ||||||
Authors | Manickam, Y. / Nirmal, N. / Suzuki, A. / Sugiyama, Y. / Yamane, T. / Devadasan, V. / Sharma, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structural analysis of actinidin and a comparison of cadmium and sulfur anomalous signals from actinidin crystals measured using in-house copper- and chromium-anode X-ray sources Authors: Yogavel, M. / Nithya, N. / Suzuki, A. / Sugiyama, Y. / Yamane, T. / Velmurugan, D. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p5v.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p5v.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 3p5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/3p5v ftp://data.pdbj.org/pub/pdb/validation_reports/p5/3p5v | HTTPS FTP |
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-Related 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: 23993.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinidia arguta (plant) / References: UniProt: A5HII2*PLUS, actinidain | ||||
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#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.28 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG 400, 0.1M sodium acetate, 30mM Cadmium chloride , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 15, 2008 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→90 Å / Num. obs: 15226 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 13 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1494 / % possible all: 100 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→19.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2161 / WRfactor Rwork: 0.1732 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8682 / SU B: 3.234 / SU ML: 0.097 / SU R Cruickshank DPI: 0.187 / SU Rfree: 0.1586 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 63.21 Å2 / Biso mean: 20.6068 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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