+Open data
-Basic information
Entry | Database: PDB / ID: 5a47 | ||||||
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Title | Structure of Thaumatin obtained by multi crystal data collection | ||||||
Components | THAUMATIN-1 | ||||||
Keywords | PLANT PROTEIN / MULTI CRYSTAL DATA COLLECTION / SYNCHROTRON SERIAL CRYSTALLOGRAPHY / SSX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THAUMATOCOCCUS DANIELLII (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.2 Å | ||||||
Authors | Zander, U. / Bourenkov, G. / Popov, A.N. / de Sanctis, D. / McCarthy, A.A. / Svensson, O. / Round, E.S. / Gordeliy, V.I. / Mueller-Dieckmann, C. / Leonard, G.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines. Authors: Zander, U. / Bourenkov, G. / Popov, A.N. / De Sanctis, D. / Svensson, O. / Mccarthy, A.A. / Round, E. / Gordeliy, V. / Mueller-Dieckmann, C. / Leonard, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a47.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a47.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a47 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a47 | 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: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THAUMATOCOCCUS DANIELLII (katemfe) / References: UniProt: P02883 |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.73 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.969 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→19.76 Å / Num. obs: 81704 / % possible obs: 99.4 % / Observed criterion σ(I): 2.8 / Redundancy: 51.3 % / Rmerge(I) obs: 0.09 |
-Processing
Software | Name: REFMAC / Version: 5.8.0103 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.944 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 mean: 15.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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