+Open data
-Basic information
Entry | Database: PDB / ID: 5yr3 | ||||||
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Title | Structure of sfYFP66BPA | ||||||
Components | Yellow fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / Bioluminescence Protein Chromophore Linkage | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Kang, F. / Wang, L. / Wang, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: sfYFP66BPA Authors: Kang, F. / Wang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yr3.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yr3.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yr3 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yr3 | HTTPS FTP |
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-Related structure data
Related structure data | 1qyoS 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: 25434.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: yfp / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A059PIR9 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE THR 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: 2.31 Å3/Da / Density % sol: 46.77 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 15% PEG 3350, 0.1M malic acid, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.434 Å / Num. obs: 19926 / % possible obs: 99.2 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.89 / Num. unique obs: 3150 / CC1/2: 0.93 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qyo Resolution: 1.901→29.432 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→29.432 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.4003 Å / Origin y: 7.8323 Å / Origin z: 22.8252 Å
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Refinement TLS group | Selection details: all |