+Open data
-Basic information
Entry | Database: PDB / ID: 2vvj | ||||||||||||
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Title | IrisFP fluorescent protein in its red form, cis conformation | ||||||||||||
Components | (Green to red photoconvertible GFP-like protein EosFP) x 2 | ||||||||||||
Keywords | FLUORESCENT PROTEIN / PHOTOACTIVATION / PHOTOCONVERSION / OPTICAL HIGHLIGHTERS / MICROSPECTROPHOTOMETRY / EOSFP / PHOTOCHROMISM / PHOTOSWITCHING | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Lobophyllia hemprichii (invertebrata) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Adam, V. / Lelimousin, M. / Boehme, S. / Desfonds, G. / Nienhaus, K. / Field, M.J. / Wiedenmann, J. / McSweeney, S. / Nienhaus, G.U. / Bourgeois, D. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structural Characterization of Irisfp, an Optical Highlighter Undergoing Multiple Photo-Induced Transformations. Authors: Adam, V. / Lelimousin, M. / Boehme, S. / Desfonds, G. / Nienhaus, K. / Field, M.J. / Wiedenmann, J. / Mcsweeney, S. / Nienhaus, G.U. / Bourgeois, D. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vvj.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vvj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 2vvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vvj ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vvj | HTTPS FTP |
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-Related structure data
Related structure data | 2vvhC 2vviC 1zuxS S: Starting model for refinement C: citing same article (ref.) |
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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: 6933.920 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q5S6Z9 #2: Protein | Mass: 19056.510 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q5S6Z9 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-SO3 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 173 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 191 TO LEU ...ENGINEERED | Sequence details | RESIDUES HIS 62, TYR 63 AND GLY 64 AUTOCATALYTICALLY FORM THE CHROMOPHORE IEY LABELLED AS RESIDUE ...RESIDUES HIS 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: 2.81 Å3/Da / Density % sol: 56.24 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.4 Details: CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, BICINE, PH 8.4, VAPOR DIFFUSION, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.816 |
Detector | Type: QUANTUM / Detector: CCD / Date: Mar 3, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.816 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.7 Å / Num. obs: 78543 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.37 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.44 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZUX Resolution: 2→45.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.269 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.158 / 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: 30.429 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.69 Å
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Refine LS restraints |
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