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Yorodumi- PDB-7z7q: Structure of the T207D single-point mutant of the fluorescent pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z7q | |||||||||
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Title | Structure of the T207D single-point mutant of the fluorescent protein NeonCyan1 at pH 6.5 | |||||||||
Components | NeonCyan1 | |||||||||
Keywords | FLUORESCENT PROTEIN / mNeonGreen / Trp-based fluorescent chromophore / rational design | |||||||||
Function / homology | Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Green fluorescent protein blFP-Y3 Function and homology information | |||||||||
Biological species | Branchiostoma lanceolatum (amphioxus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Duarte, K. / Dupuy, J. / Royant, A. | |||||||||
Funding support | France, United States, 2items
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Citation | Journal: Protein Eng.Des.Sel. / Year: 2022 Title: Cyan fluorescent proteins derived from mNeonGreen. Authors: Zarowny, L. / Clavel, D. / Johannson, R. / Duarte, K. / Depernet, H. / Dupuy, J. / Baker, H. / Brown, A. / Royant, A. / Campbell, R.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z7q.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z7q.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 7z7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/7z7q ftp://data.pdbj.org/pub/pdb/validation_reports/z7/7z7q | HTTPS FTP |
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-Related structure data
Related structure data | 7z7oC 7z7pC 5ltrS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 26656.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Residue CRC69 is formed by the autocatalytic cyclisation of the consecutive amino acid residues GWG, hence the mismatch in the sequence alignment Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Gene: blFP-Y3 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PNC0 #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 grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM HEPES pH 6.5 and 22% PEG8000 (w/v) |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019 |
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.06 Å / Num. obs: 85638 / % possible obs: 86.7 % / Redundancy: 1.7 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.109 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8266 / CC1/2: 0.703 / Rrim(I) all: 0.754 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LTR Resolution: 1.6→40.06 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.136 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 52.44 Å2 / Biso mean: 15.588 Å2 / Biso min: 4.1 Å2
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Refinement step | Cycle: final / Resolution: 1.6→40.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Rfactor Rfree error: 0
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