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Yorodumi- PDB-3ztf: X-ray Structure of the Cyan Fluorescent Protein mTurquoise2 (K206... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ztf | ||||||
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Title | X-ray Structure of the Cyan Fluorescent Protein mTurquoise2 (K206A mutant) | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | FLUORESCENT PROTEIN / CFP / FRET / FRET DONOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | AEQUOREA VICTORIA (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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: Nat.Methods / Year: 2010 Title: Bright Cyan Fluorescent Protein Variants Identified by Fluorescence Lifetime Screening. Authors: Goedhart, J. / van Weeren, L. / Hink, M.A. / Vischer, N.O.E. / Jalink, K. / Gadella, T.W.J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ztf.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ztf.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ztf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/3ztf ftp://data.pdbj.org/pub/pdb/validation_reports/zt/3ztf | HTTPS FTP |
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-Related structure data
Related structure data | 2ydzC 2ye0SC 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: 27700.178 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-238 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHROMOPHORE RESULTING FROM THE AUTOCATALYTIC CYCLISATION OF RESIDUES 65 TO 67 (SWG) Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / 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, TYR 66 TO TRP ...ENGINEERED |
-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: 40 % Description: DATA WERE RECORDED USING THE ESRF HELICAL DATA COLLECTION PROCEDURE |
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Crystal grow | pH: 7.25 Details: 30 MG/ML PROTEIN, 19% PEG 8000, 100 MM MGCL2, 100 MM HEPES PH 7.25 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2011 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→46.7 Å / Num. obs: 52472 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.31→1.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YE0 Resolution: 1.31→35.18 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.73 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.05 / 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: 19.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→35.18 Å
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Refine LS restraints |
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