+Open data
-Basic information
Entry | Database: PDB / ID: 3w1d | ||||||
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Title | Structure of a pressure sensitive YFP variant YFP-G3 | ||||||
Components | Green Fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / fluorescent protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Imada, K. / Yoshizawa, K. / Kinoshita, M. / Watanabe, T.M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Glycine insertion makes yellow fluorescent protein sensitive to hydrostatic pressure. Authors: Watanabe, T.M. / Imada, K. / Yoshizawa, K. / Nishiyama, M. / Kato, C. / Abe, F. / Morikawa, T.J. / Kinoshita, M. / Fujita, H. / Yanagida, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w1d.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w1d.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3w1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/3w1d ftp://data.pdbj.org/pub/pdb/validation_reports/w1/3w1d | HTTPS FTP |
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-Related structure data
Related structure data | 3w1cC 3dq7S 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: 27046.463 Da / Num. of mol.: 1 / Mutation: S65G, V68L, S72A, T206Y, H234L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pAL7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 (DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 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: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 13-17% PEG 8000, 0.1M Bis-Tris buffer, 200-400mM calcium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 12, 2010 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→21.3 Å / Num. all: 36353 / Num. obs: 36353 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4827 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DQ7 Resolution: 1.5→21.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1202885.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7126 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→21.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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