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Yorodumi- PDB-4q7r: Crystal structure of large Stokes shift fluorescent protein LSSmOrange -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q7r | ||||||
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Title | Crystal structure of large Stokes shift fluorescent protein LSSmOrange | ||||||
Components | LSSmOrange | ||||||
Keywords | FLUORESCENT PROTEIN / beta-barrel / large Stokes shift fluorescent protein / chromophore | ||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / metal ion binding Similarity search - Function | ||||||
Biological species | Discosoma sp. (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Pletnev, S. / Dauter, Z. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Orange Fluorescent Proteins: Structural Studies of LSSmOrange, PSmOrange and PSmOrange2. Authors: Pletnev, S. / Shcherbakova, D.M. / Subach, O.M. / Pletneva, N.V. / Malashkevich, V.N. / Almo, S.C. / Dauter, Z. / Verkhusha, V.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q7r.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7r.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 4q7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q7r_validation.pdf.gz | 462.7 KB | Display | wwPDB validaton report |
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Full document | 4q7r_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 4q7r_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 4q7r_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7r ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7r | HTTPS FTP |
-Related structure data
Related structure data | 4q7tC 4q7uC 2h5oS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 28120.748 Da / Num. of mol.: 2 / Mutation: R17H, V44A, F83L, W143M, I161D, M163L, G196D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: D0VWW2 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Sequence details | RESIDUES PHE65, GLY66, TYR67, AND GLY68 CIRCULARIZ | |
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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: 1.98 Å3/Da / Density % sol: 37.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2 M zinc acetate, 0.1 M acetate buffer, 20% PEG1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.4→55.335 Å / Num. obs: 84546 / % possible obs: 98.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.056 / Χ2: 1.014 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H5O Resolution: 1.4→55.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1763 / WRfactor Rwork: 0.153 / FOM work R set: 0.9086 / SU B: 1.922 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0633 / SU Rfree: 0.0555 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.056 / 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 max: 94.67 Å2 / Biso mean: 18.796 Å2 / Biso min: 6.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→55.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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