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Yorodumi- PDB-5amz: Crystal Structure of Thaumatin processed with the CrystalDirect a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5amz | ||||||
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Title | Crystal Structure of Thaumatin processed with the CrystalDirect automated mounting and cryo-cooling technology | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO-COOLING / CRYSTALDIRECT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å | ||||||
Authors | Zander, U. / Hoffmann, G. / Cornaciu, I. / Cipriani, F. / Marquez, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation. Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5amz.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amz.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 5amz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amz ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amz | HTTPS FTP |
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-Related structure data
Related structure data | 5amwC 5amxC 5an4C 5andC 5aneC 5angC 5aniC 5anjC 5ankC 5anlC 5anoC 5dwpC 5ebhC C: citing same article (ref.) |
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Similar 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: 22155.980 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 50733 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.07 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.056 / 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: 17.874 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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