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Yorodumi- PDB-8ths: Crystal Structure of a reconstructed Kaede-type Red Fluorescent P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ths | ||||||
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Title | Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA A69T | ||||||
Components | KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T | ||||||
Keywords | FLUORESCENT PROTEIN / BETA BARREL / LUMINESCENT PROTEIN | ||||||
Function / homology | NITRATE ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Henderson, J.N. / Mills, J.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Chem / Year: 2023 Title: Capturing excited-state structural snapshots of evolutionary green-to-red photochromic fluorescent proteins. Authors: Krueger, T.D. / Henderson, J.N. / Breen, I.L. / Zhu, L. / Wachter, R.M. / Mills, J.H. / Fang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ths.cif.gz | 378.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ths.ent.gz | 308.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ths.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/8ths ftp://data.pdbj.org/pub/pdb/validation_reports/th/8ths | HTTPS FTP |
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-Related structure data
Related structure data | 8ub6C 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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Unit cell |
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-Components
#1: Protein | Mass: 26464.092 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star #2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-PEG / #4: 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: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 microliters of protein at 20 mg/mL in 10 mM HEPES pH 7.5 + 75 mM NaCl mixed with 2 microliters of well solution containing 35% PEG 3350 + 0.3 M potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.74 Å / Num. obs: 152026 / % possible obs: 99.8 % / Redundancy: 7.8 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Χ2: 0.99 / Net I/σ(I): 18.3 / Num. measured all: 1183642 |
Reflection shell | Resolution: 1.5→1.53 Å / % possible obs: 97.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 1.814 / Num. measured all: 33660 / Num. unique obs: 7274 / CC1/2: 0.331 / Rpim(I) all: 0.927 / Rrim(I) all: 2.05 / Χ2: 0.95 / Net I/σ(I) obs: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.03 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.165 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.493 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→47.03 Å
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