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Yorodumi- PDB-3ssp: Engineered low-affinity halide-binding protein derived from YFP: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ssp | |||||||||
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Title | Engineered low-affinity halide-binding protein derived from YFP: halide-free | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | HALIDE BINDING PROTEIN / beta barrel / luminescent protein / yellow fluorescent protein / imaging reagent | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.628 Å | |||||||||
Authors | Wang, W. / Grimley, J.S. / Beese, L.S. / Hellinga, H.W. | |||||||||
Citation | Journal: To be Published Title: Determination of engineered chloride-binding site structures in fluorescent proteins reveals principles of halide recognition Authors: Wang, W. / Grimley, J.S. / Augustine, G.J. / Beese, L.S. / Hellinga, H.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ssp.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ssp.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ssp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/3ssp ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3ssp | HTTPS FTP |
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-Related structure data
Related structure data | 3sryC 3ss0C 3sshC 3sskC 3sslC 3sstSC 3ssvC 3ssyC 3svbC 3svcC 3svdC 3sveC 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: 29362.801 Da / Num. of mol.: 1 / Mutation: S72A, K79R, T203Y, H231L Source method: isolated from a genetically manipulated source Details: synthetic / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | UNP RESIDUE SER65 UNDERWENT MUTATION TO GLY. GLY65, TYR66, AND GLY67 CIRCULARIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.49 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14% PEG4000, 50 mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.628→41.311 Å / Num. obs: 27845 / % possible obs: 96.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Χ2: 1.535 / Net I/σ(I): 17.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3SST Resolution: 1.628→39.658 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 15.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.722 Å2 / ksol: 0.424 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.19 Å2 / Biso mean: 16.7294 Å2 / Biso min: 4.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.628→39.658 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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