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Yorodumi- PDB-7lsd: Crystal structure of near-infrared fluorescent protein miRFP718nano -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lsd | ||||||
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Title | Crystal structure of near-infrared fluorescent protein miRFP718nano | ||||||
Components | miRFP718nano | ||||||
Keywords | FLUORESCENT PROTEIN / near-infrared fluorescent protein / miRFP / miRFPnano / phytochrome / BphP / cyanobacterichrome / CBCR | ||||||
Function / homology | BILIVERDINE IX ALPHA Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Pletnev, S. | ||||||
Citation | Journal: To Be Published Title: Rational design of a small near-infrared fluorescent protein from CBCR suitable for deep-tissue SWIR imaging. Authors: Oliinyk, O.S. / Pletnev, S. / Ma, C. / Baloban, M. / Toboada, C. / Sheng, H. / Yao, J. / Verkhusha, V.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lsd.cif.gz | 157.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lsd.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lsd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7lsd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7lsd_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 7lsd_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/7lsd ftp://data.pdbj.org/pub/pdb/validation_reports/ls/7lsd | HTTPS FTP |
-Related structure data
Related structure data | 6mghS S: Starting model for refinement |
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Similar 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: 18828.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-BLA / #3: 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: 2.72 Å3/Da / Density % sol: 54.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 12.6% PEG6000, 0.1 M lithium sulfate, 0.07 M citric acid, pH 3.5, 2.1% D-sorbitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. obs: 80892 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Χ2: 0.616 / Net I/σ(I): 10.3 / Num. measured all: 285750 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MGH Resolution: 1.7→29.84 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.358 / SU ML: 0.074 / SU R Cruickshank DPI: 0.0893 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.093 / 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: 100.38 Å2 / Biso mean: 26.701 Å2 / Biso min: 14.07 Å2
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Refinement step | Cycle: final / Resolution: 1.7→29.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.741 Å / Rfactor Rfree error: 0
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