+Open data
-Basic information
Entry | Database: PDB / ID: 2blu | ||||||
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Title | Thaumatin After A High Dose X-Ray "Burn" | ||||||
Components | THAUMATIN I | ||||||
Keywords | PLANT PROTEIN / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / TASTE-MODIFYING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THAUMATOCOCCUS DANIELLII (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å | ||||||
Authors | Nanao, M.H. / Ravelli, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Improving Radiation-Damage Substructures for Rip. Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2blu.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2blu.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 2blu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2blu_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 2blu_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 2blu_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2blu_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/2blu ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2blu | HTTPS FTP |
-Related structure data
Related structure data | 2bloC 2blpC 2blqC 2blrC 2blvC 2blwC 2blxC 2blyC 2blzC 2bn1C 2bn3C 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 / Fragment: RESIDUES 1-206 / 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 / |
Compound details | TASTE-MODIFYING PROTEIN; INTENSELY SWEET-TASTING. IT IS 100000 TIMES SWEETER THAN SUCROSE ON A MOLAR BASIS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Details: 0.9 M SODIUM/POTASSIUM TARTRATE, 0.1 M HEPES, PH 7.3, 15 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9392 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 93941 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.38 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.35 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.264 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→45 Å
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Refine LS restraints |
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