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Yorodumi- PDB-4as8: X-ray structure of the cyan fluorescent protein Cerulean cryoprot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4as8 | ||||||
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Title | X-ray structure of the cyan fluorescent protein Cerulean cryoprotected with ethylene glycol | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | FLUORESCENT PROTEIN / FRET | ||||||
Function / homology | Function and homology information | ||||||
Biological species | AEQUOREA VICTORIA (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | von Stetten, D. / Batot, G. / Noirclerc-Savoye, M. / Royant, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Alteration of Fluorescent Protein Spectroscopic Properties Upon Cryoprotection Authors: von Stetten, D. / Batot, G. / Noirclerc-Savoye, M. / Royant, A. | ||||||
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 | 4as8.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4as8.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 4as8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/4as8 ftp://data.pdbj.org/pub/pdb/validation_reports/as/4as8 | HTTPS FTP |
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-Related structure data
Related structure data | 2wsoS 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: 27618.119 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHROMOPHORE RESULTING FROM THE AUTOCATALYTIC CYCLISATION OF RESIDUES 65 TO 67 Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: P42212 | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.68 % Description: DATA WAS RECORDED USING THE ESRF HELICAL DATA COLLECTION PROCEDURE. |
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Crystal grow | pH: 7.25 Details: 13 MG/ML PROTEIN, 14% PEG8000, 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: 0.97926 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2011 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→46.7 Å / Num. obs: 112014 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.02→1.08 Å / Redundancy: 2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WSO Resolution: 1.02→46.75 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.529 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.02 / 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: 10.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.02→46.75 Å
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Refine LS restraints |
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