+Open data
-Basic information
Entry | Database: PDB / ID: 5kvw | |||||||||||||||
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Title | T. danielli thaumatin at 100K, Data set 1 | |||||||||||||||
Components | Thaumatin-1 | |||||||||||||||
Keywords | PLANT PROTEIN / Conformational variation / Radiation damage | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Thaumatococcus daniellii (katemfe) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | |||||||||||||||
Authors | Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J Synchrotron Radiat / Year: 2017 Title: Conformational variation of proteins at room temperature is not dominated by radiation damage. Authors: Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kvw.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kvw.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kvw_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 5kvw_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 5kvw_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5kvw_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/5kvw ftp://data.pdbj.org/pub/pdb/validation_reports/kv/5kvw | HTTPS FTP |
-Related structure data
Related structure data | 5kulC 5kunC 5kuoC 5kuqC 5kurC 5kusC 5kuuC 5kuvC 5kuwC 5kuzC 5kv0C 5kv1C 5kv2C 5kv3C 5kv4C 5kv5C 5kv6C 5kv7C 5kvxC 5kvzC 5kw0C 5kw3C 5kw4C 5kw5C 5kw7C 5kw8C 5kxkC 5kxlC 5kxmC 5kxnC 5kxoC 5kxpC 5kxrC 5kxsC 5kxtC 5kxwC 5kxxC 5kxyC 5kxzC 5ky1C 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
#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: Chemical | #4: 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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) ...Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) IN THE SITTING DROP FORMAT. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.21549 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 13, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.21549 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→31.613 Å / Num. all: 34655 / Num. obs: 34655 / % possible obs: 99 % / Redundancy: 4.1 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Rsym value: 0.044 / Net I/av σ(I): 10.091 / Net I/σ(I): 15.1 / Num. measured all: 141558 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RQW Resolution: 1.59→31.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.358 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 92.94 Å2 / Biso mean: 26.895 Å2 / Biso min: 14.56 Å2
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Refinement step | Cycle: final / Resolution: 1.59→31.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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