+Open data
-Basic information
Entry | Database: PDB / ID: 4h47 | ||||||
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Title | 1.9 angstrom CyPet structure at pH5.2 | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / beta barrel / luminescence | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hu, X.-J. / Liu, R. | ||||||
Citation | Journal: To be Published Title: Structural insights of the fluorescent states of CyPet Authors: Liu, R. / Zhou, Y.-B. / Ding, Y. / Hu, X.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h47.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h47.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 4h47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h47_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
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Full document | 4h47_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 4h47_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4h47_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/4h47 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/4h47 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 26887.344 Da / Num. of mol.: 1 / Mutation: T9G, V11I, D19E, A87V, I167A, E172T, L194I 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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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Sequence details | (1) RESIDUES SER 65, TYR 66 HAVE BEEN MUTATED TO THR 65, TRP 66. RESIDUES THR 65, TRP 66 AND GLY 67 ...(1) RESIDUES SER 65, TYR 66 HAVE BEEN MUTATED TO THR 65, TRP 66. RESIDUES THR 65, TRP 66 AND GLY 67 CONSTITUTE |
-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: 41.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 30% PEG 4000, 0.1M Sodium Acetate, 0.2M Lithium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.96 Å / Num. all: 18366 / Num. obs: 17577 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2434 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.024 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.157 / ESU R Free: 0.167 / 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: 28.792 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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