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Yorodumi- PDB-6fj9: Structure of Thaumatin collected from an in situ crystal on ID30B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fj9 | ||||||
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Title | Structure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV. | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | McCarthy, A.A. / Mueller-Dieckmann, C. | ||||||
Citation | Journal: J Synchrotron Radiat / Year: 2018 Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fj9.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fj9.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/6fj9 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/6fj9 | HTTPS FTP |
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-Related structure data
Related structure data | 6fidC 6fj2C 6fj4C 6fj6C 6fj8C 5a47S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/547 / Data set type: diffraction image 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 genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % / Description: Bipyramidal crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES and 0.7 M potassium/sodium tartrate |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.7085 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2016 Details: Be CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing) |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7085 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→54.63 Å / Num. obs: 39794 / % possible obs: 92.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1988 / CC1/2: 0.6 / Rpim(I) all: 0.518 / Rrim(I) all: 0.979 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5a47 Resolution: 1.5→54.63 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.533 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.775 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→54.63 Å
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Refine LS restraints |
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