+Open data
-Basic information
Entry | Database: PDB / ID: 1ly0 | ||||||
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Title | Structure of thaumatin crystallized in the presence of glycerol | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / TASTE-MODIFYING PROTEIN / SWEET PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Charron, C. / Kadri, A. / Robert, M.C. / Giege, R. / Lorber, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin. Authors: Charron, C. / Kadri, A. / Robert, M.C. / Giege, R. / Lorber, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ly0.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ly0.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ly0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1ly0 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1ly0 | HTTPS FTP |
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-Related structure data
Related structure data | 1lxzC 1thwS 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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Details | The biological unit is a monomer |
-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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 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: LURE / Beamline: DW32 / Wavelength: 0.9474 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9474 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→30 Å / Num. all: 55721 / Num. obs: 55482 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.049 |
Reflection shell | Resolution: 1.36→1.41 Å / Rsym value: 0.151 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1THW Resolution: 1.36→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.36→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.41 Å
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