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Yorodumi- PDB-2ie2: The 1.7 A crystal structure of Dronpa: a photoswitchable green fl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ie2 | |||||||||
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Title | The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein | |||||||||
Components | Fluorescent protein DronpaFluorescence | |||||||||
Keywords | LUMINESCENT PROTEIN / BETA BARREL | |||||||||
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: 1.7 Å | |||||||||
Authors | Rossjohn, J. / Wilmann, P.G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The 1.7 A Crystal Structure of Dronpa: A Photoswitchable Green Fluorescent Protein Authors: Wilmann, P.G. / Turcic, K. / Battad, J.M. / Wilce, M.C.J. / Devenish, R.J. / Prescott, M. / Rossjohn, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ie2.cif.gz | 271.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ie2.ent.gz | 219.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ie2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2ie2 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2ie2 | HTTPS FTP |
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-Related structure data
Related structure data | 1xssS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25497.904 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Plasmid: pQE10N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5TLG6 #2: Water | ChemComp-HOH / | Sequence details | RESIDUES CYS 62, TYR 63 AND GLY 64 AUTOCATALYTICALLY FORM THE CHROMOPHORE GYC LABELLED AS RESIDUE ...RESIDUES CYS 62, TYR 63 AND GLY 64 AUTOCATALY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 23% PEG 3350, 0.1M Tris, 0.1M Magnesium Chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→89.09 Å / Num. obs: 129416 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.704→1.748 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.573 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XSS Resolution: 1.7→89.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.119 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.13 / ESU R Free: 0.116 / 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: 19.289 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→89.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.704→1.748 Å / Total num. of bins used: 20
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