+Open data
-Basic information
Entry | Database: PDB / ID: 3n02 | ||||||
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Title | Thaumatic crystals grown in loops/micromounts | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / Crystals on loops / Thaumatin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mathes, I.I. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2010 Title: Diffraction study of protein crystals grown in cryoloops and micromounts. Authors: Berger, M.A. / Decker, J.H. / Mathews, I.I. #1: 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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Improving radiation-damage substructures for RIP. Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n02.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n02.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n02_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 3n02_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 3n02_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3n02_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/3n02 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/3n02 | HTTPS FTP |
-Related structure data
Related structure data | 3mzqC 3mzrC 3n03C 3n0bC 3n0cC 1ly0S 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
#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: Chemical | #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: 56.75 % |
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Crystal grow | Temperature: 295 K / Method: crystals grown in loop/micromounts / pH: 7.3 Details: 0.9M Sodium/potassium tartrate, 0.1M HEPES (pH 7.3), 15% glycerol, Crystals grown in loop/micromounts, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 10, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29 Å / Num. all: 41945 / Num. obs: 41945 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 3.16 / Num. unique all: 3046 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LY0 Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.865 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R Free: 0.057 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.403 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.249 Å / Origin y: 24.0077 Å / Origin z: 32.8219 Å
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