+Open data
-Basic information
Entry | Database: PDB / ID: 5yr2 | ||||||
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Title | Structure of cpGFP66BPA | ||||||
Components | Green 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: 1.799 Å | ||||||
Authors | Wang, L. / Kang, F. / Wang, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of cpGFP66BPA Authors: Wang, L. / Kang, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yr2.cif.gz | 214.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yr2.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 5yr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yr2 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yr2 | HTTPS FTP |
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-Related structure data
Related structure data | 1gflS S: Starting model for refinement |
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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: 27953.359 Da / Num. of mol.: 2 / Mutation: Y163(BPA) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Plasmid: PET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A059PIQ0 #2: Water | ChemComp-HOH / | Sequence details | UNP residue TYR 66 has been mutated to unnatural amino acid named 4-Benzoyl-L-phenylalanine. 3 ...UNP residue TYR 66 has been mutated to unnatural amino acid named 4-Benzoyl-L-phenylalanine. 3 residues THR, 4-Benzoyl-L-phenylalanine, GLY constitute the chromophore BF9 163. | |
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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: 2.09 Å3/Da / Density % sol: 37.38 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350 25%, 0.2M MgCl2,0.1M Bis-Tris pH 5.5 |
-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: Nov 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→50 Å / Num. obs: 39464 / % possible obs: 98.5 % / Redundancy: 5.6 % / CC1/2: 0.996 / Net I/σ(I): 21.17 |
Reflection shell | Resolution: 1.799→1.86 Å / Redundancy: 5.6 % / Num. unique obs: 3883 / CC1/2: 0.912 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GFL Resolution: 1.799→39.183 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→39.183 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: 11.4803 Å / Origin y: -7.5192 Å / Origin z: 91.5958 Å
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Refinement TLS group | Selection details: all |