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Yorodumi- PDB-2ydz: X-ray structure of the cyan fluorescent protein SCFP3A (K206A mutant) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ydz | ||||||
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Title | X-ray structure of the cyan fluorescent protein SCFP3A (K206A mutant) | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | FLUORESCENT PROTEIN / FRET DONOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | AEQUOREA VICTORIA (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | von Stetten, D. / Goedhart, J. / Noirclerc-Savoye, M. / Lelimousin, M. / Joosen, L. / Hink, M.A. / van Weeren, L. / Gadella, T.W.J. / Royant, A. | ||||||
Citation | Journal: Nat.Commun / Year: 2012 Title: Structure-Guided Evolution of Cyan Fluorescent Proteins Towards a Quantum Yield of 93% Authors: Goedhart, J. / von Stetten, D. / Noirclerc-Savoye, M. / Lelimousin, M. / Joosen, L. / Hink, M.A. / van Weeren, L. / Gadella, T.W.J. / Royant, A. #1: Journal: Biochemistry / Year: 2006 Title: Cyan and Yellow Super Fluorescent Proteins with Improved Brightness, Protein Folding, and Fret Forster Radius. Authors: Kremers, G. / Goedhart, J. / van Munster, E.B. / Gadella, T.W.J.J. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ydz.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ydz.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2ydz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2ydz ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2ydz | HTTPS FTP |
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-Related structure data
Related structure data | 2ye0C 3ztfC 2wsoS 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: 27680.188 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR(DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, SER 65 TO THR ...ENGINEERED |
Sequence details | CHROMOPHORE RESULTING FROM AUTOCATALYTIC CYCLIZATION OF CONSECUTIVE AMINO ACID RESIDUES THR65, ...CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % Description: DATA WERE RECORDED USING THE ESRF HELICAL DATA COLLECTION PROCEDURE. |
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Crystal grow | pH: 6.75 Details: 16 MG/ML PROTEIN, 13% PEG8000, 100 MM MGCL2, 100 MM HEPES PH 6.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.033 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 4, 2010 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→46.4 Å / Num. obs: 29189 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WSO Resolution: 1.59→46.41 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.307 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.085 / 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 mean: 19.736 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→46.41 Å
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Refine LS restraints |
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