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Yorodumi- PDB-8ub6: Crystal Structure of a reconstructed Kaede-type Red Fluorescent P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ub6 | ||||||
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Title | Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA H62X, containing 3-methylhistidine at position 62 | ||||||
Components | LEAST EVOLVED ANCESTOR (LEA) GFP-LIKE PROTEINS | ||||||
Keywords | LUMINESCENT PROTEIN / BETA BARREL | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 8ub6.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ub6.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ub6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ub6_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 8ub6_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 8ub6_validation.xml.gz | 11 KB | Display | |
Data in CIF | 8ub6_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/8ub6 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/8ub6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26525.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1:1 ratio of well solution (25% PEG + 0.2 M MgCl2) and protein solution (LEA H62X at 15 mg/mL in 10 mM HEPES pH 7.5 + 75 mM NaCl). |
-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: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.59 Å / Num. obs: 24128 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Χ2: 1.02 / Net I/σ(I): 18.8 / Num. measured all: 209736 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 99.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 3.987 / Num. measured all: 10899 / Num. unique obs: 1279 / CC1/2: 0.367 / Rpim(I) all: 1.425 / Rrim(I) all: 4.242 / Χ2: 0.98 / Net I/σ(I) obs: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 9.787 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.116 / 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: 44.299 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→39.97 Å
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Refine LS restraints |
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