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Yorodumi- PDB-4rys: Crystal structure of the green fluorescent rotein NowGFP (the var... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rys | ||||||
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Title | Crystal structure of the green fluorescent rotein NowGFP (the variant of cyan Cerulean) at pH 4.8 | ||||||
Components | NowGFP | ||||||
Keywords | FLUORESCENT PROTEIN / NowGFP / TWG chromophore / beta-barrel / variant of cyan Cerulean | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | ||||||
Biological species | CFP MARKER PLASMID PWM1009 (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Pletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore. Authors: Pletnev, V.Z. / Pletneva, N.V. / Sarkisyan, K.S. / Mishin, A.S. / Lukyanov, K.A. / Goryacheva, E.A. / Ziganshin, R.H. / Dauter, Z. / Pletnev, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rys.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rys.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4rys ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4rys | HTTPS FTP |
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-Related structure data
Related structure data | 4rtcC 4rywC 2wsoS 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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1 |
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Unit cell |
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Details | One monomer in assymetric unit |
-Components
#1: Protein | Mass: 27204.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CFP MARKER PLASMID PWM1009 (others) / Production host: Escherichia coli (E. coli) | ||
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#2: Chemical | ChemComp-GOL / #3: 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: 3.05 Å3/Da / Density % sol: 59.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 14mM KH2PO4, pH 4.8, 14% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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: 2014 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.18→50 Å / Num. obs: 107191 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.904 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WSO Resolution: 1.18→26.19 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1465 / WRfactor Rwork: 0.133 / FOM work R set: 0.9091 / SU R Cruickshank DPI: 0.026 / SU Rfree: 0.0252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.025 / 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 max: 135.06 Å2 / Biso mean: 15.798 Å2 / Biso min: 4.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→26.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.179→1.209 Å / Total num. of bins used: 20
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