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Yorodumi- PDB-4en1: The 1.62A structure of a FRET-optimized Cerulean Fluorescent Protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 4en1 | ||||||
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Title | The 1.62A structure of a FRET-optimized Cerulean Fluorescent Protein | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / GFP-like beta-barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Watkins, J.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: The 1.6 A resolution structure of a FRET-optimized Cerulean fluorescent protein. Authors: Watkins, J.L. / Kim, H. / Markwardt, M.L. / Chen, L. / Fromme, R. / Rizzo, M.A. / Wachter, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4en1.cif.gz | 118.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4en1.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 4en1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/4en1 ftp://data.pdbj.org/pub/pdb/validation_reports/en/4en1 | 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29589.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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-Non-polymers , 5 types, 365 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES SER 65, TYR 66 OF THE GREEN FLUORESCENT PROTEIN SEQUENCE (UNP ENTRY P42212) WERE MUTATED ...RESIDUES SER 65, TYR 66 OF THE GREEN FLUORESCEN |
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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: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 298 K / pH: 4.7 Details: mother liquor consisting of 0.08 M sodium acetate trihydrate, 0.16 M ammonium sulfate, 9% (w/v) PEG4000, and 19% (v/v) glycerol. Hanging drops contained 2 uL protein solution and 1 uL mother ...Details: mother liquor consisting of 0.08 M sodium acetate trihydrate, 0.16 M ammonium sulfate, 9% (w/v) PEG4000, and 19% (v/v) glycerol. Hanging drops contained 2 uL protein solution and 1 uL mother liquor, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2011 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 79895 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.04 / Rsym value: 0.477 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WSO Resolution: 1.62→29.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.461 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 21.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.66 Å / Total num. of bins used: 20
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