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Yorodumi- PDB-4uts: Room temperature crystal structure of the fast switching M159T mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uts | |||||||||
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Title | Room temperature crystal structure of the fast switching M159T mutant of fluorescent protein Dronpa | |||||||||
Components | FLUORESCENT PROTEIN DRONPA | |||||||||
Keywords | FLUORESCENT PROTEIN / PHOTOSWITCHING / PHOTOCHROMIC | |||||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ECHINOPHYLLIA SP. SC22 (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Kaucikas, M. / Fitzpatrick, A. / Bryan, E. / Struve, A. / Henning, R. / Kosheleva, I. / Srajer, V. / van Thor, J.J. | |||||||||
Citation | Journal: Proteins / Year: 2015 Title: Room Temperature Crystal Structure of the Fast Switching M159T Mutant of the Fluorescent Protein Dronpa. Authors: Kaucikas, M. / Fitzpatrick, A. / Bryan, E. / Struve, A. / Henning, R. / Kosheleva, I. / Srajer, V. / Groenhof, G. / Van Thor, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uts.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uts.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uts_validation.pdf.gz | 332.2 KB | Display | wwPDB validaton report |
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Full document | 4uts_full_validation.pdf.gz | 340.3 KB | Display | |
Data in XML | 4uts_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 4uts_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4uts ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4uts | HTTPS FTP |
-Related structure data
Related structure data | 2z1oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24511.645 Da / Num. of mol.: 4 / Fragment: FLUORESCENT PROTEIN, RESIDUES 2-217 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ECHINOPHYLLIA SP. SC22 (invertebrata) / Plasmid: PRSET / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: Q5TLG6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 22 % (W/V) PEG (POLY[ETHYLENE GLYCOL]) MONOMETHYL ETHER 3350 AND 0.14 M MG(NO3)2, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2013 / Details: BENT CONICAL SI-MIRROR (RH COATED) |
Radiation | Monochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→55.82 Å / Num. obs: 810104 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.04→2.15 Å / Redundancy: 7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.9 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z1O Resolution: 2.03→55.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.856 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / 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 mean: 36.625 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→55.63 Å
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Refine LS restraints |
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