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Yorodumi- PDB-3e0a: Thaumatin by Classical hanging drop method after high X-Ray dose ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e0a | ||||||
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Title | Thaumatin by Classical hanging drop method after high X-Ray dose on ESRF ID29 beamline | ||||||
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: 1.51 Å | ||||||
Authors | Tripathi, S. / Pechkova, E. / Nicolini, C. | ||||||
Citation | Journal: To be Published Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective Authors: Pechkova, E. / Tripathi, S. / Nicolini, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e0a.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e0a.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e0a_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 3e0a_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 3e0a_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3e0a_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0a ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0a | HTTPS FTP |
-Related structure data
Related structure data | 3dnzC 3do0C 3do1C 3do2C 3dvqC 3dvrC 3dvsC 3dw1C 3dw3C 3dweC 3dznC 3dzpC 3dzrC 1rqwS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22243.119 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % / Mosaicity: 0.25 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM ADA, 1M Na/K-tartrate, 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: ESRF / Beamline: ID29 / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2007 / Details: toroidal mirror |
Radiation | Monochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→54.074 Å / Num. obs: 32305 / % possible obs: 78.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 |
Reflection shell | Resolution: 1.51→1.59 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.2 / Num. measured all: 1832 / Num. unique all: 1407 / Rsym value: 0.225 / % possible all: 24.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RQW Resolution: 1.51→54.07 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.903 / SU B: 2.259 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 138.6 Å2 / Biso mean: 22.373 Å2 / Biso min: 8.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→54.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Total num. of bins used: 20
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