+Open data
-Basic information
Entry | Database: PDB / ID: 8dpd | ||||||
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Title | superfolder GFP Tyr74pCNPhe mutant | ||||||
Components | Superfolder green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / unnatural amino acid / cyanophenylalanine | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / CARBON DIOXIDE / DI(HYDROXYETHYL)ETHER / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Phillips-Piro, C.M. / Papoutsis, B. / Piacentini, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Superfolder GFP Tyr74pCNPhe mutant Authors: Phillips-Piro, C.M. / Papoutsis, B. / Piacentini, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dpd.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dpd.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 8dpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/8dpd ftp://data.pdbj.org/pub/pdb/validation_reports/dp/8dpd | HTTPS FTP |
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-Related structure data
Related structure data | 2b3pS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26907.336 Da / Num. of mol.: 1 Mutation: S30R, Y39N, F64L, Q80R, F99S, N105T, Y145F, M153T, V163A, I171V, A206V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 10 beta / References: UniProt: P42212 |
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-Non-polymers , 5 types, 237 molecules
#2: Chemical | ChemComp-CO2 / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→19.9 Å / Num. obs: 37289 / % possible obs: 99.2 % / Redundancy: 8.3 % / Biso Wilson estimate: 23.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.51→1.55 Å / Mean I/σ(I) obs: 7.7 / Num. unique obs: 1762 / CC1/2: 0.572 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 1.51→19.9 Å / SU ML: 0.2107 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3979 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→19.9 Å
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Refine LS restraints |
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LS refinement shell |
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