+Open data
-Basic information
Entry | Database: PDB / ID: 8dhr | ||||||
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Title | An ester mutant of SfGFP | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / beta barrel / ester mutant | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Reddi, R. / Valiyaveetil, F.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds. Authors: Reddi, R. / Chatterjee, S. / Matulef, K. / Gustafson, A. / Gao, L. / Valiyaveetil, F.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dhr.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dhr.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/8dhr ftp://data.pdbj.org/pub/pdb/validation_reports/dh/8dhr | HTTPS FTP |
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-Related structure data
Related structure data | 8thnC 2b3pS S: Starting model for refinement C: citing same article (ref.) |
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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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27773.193 Da / Num. of mol.: 2 Mutation: R30S, N39Y, L64F, R80Q, S99F, T105N, F145Y, T153M, A163V, V171I, V206A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 #2: Water | ChemComp-HOH / | 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: 1.93 Å3/Da / Density % sol: 36.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM Hepes, pH 7.5 and 25% Peg4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.15 Å / Num. obs: 42753 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.54 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2475 / CC1/2: 0.84 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 1.75→44.08 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.19 / Stereochemistry target values: ML
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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 max: 66.65 Å2 / Biso mean: 16.0848 Å2 / Biso min: 3.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→44.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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