+Open data
-Basic information
Entry | Database: PDB / ID: 7dnb | ||||||
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Title | Crystal structure of PhoCl barrel | ||||||
Components | PhoCl Barrel | ||||||
Keywords | FLUORESCENT PROTEIN / PhoCl / Photocleavable / GFP | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Wen, Y. / Lemieux, J.M. | ||||||
Citation | Journal: Chem Sci / Year: 2021 Title: Photocleavable proteins that undergo fast and efficient dissociation. Authors: Lu, X. / Wen, Y. / Zhang, S. / Zhang, W. / Chen, Y. / Shen, Y. / Lemieux, M.J. / 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 | 7dnb.cif.gz | 253.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dnb.ent.gz | 198.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dnb_validation.pdf.gz | 804.3 KB | Display | wwPDB validaton report |
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Full document | 7dnb_full_validation.pdf.gz | 819 KB | Display | |
Data in XML | 7dnb_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 7dnb_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/7dnb ftp://data.pdbj.org/pub/pdb/validation_reports/dn/7dnb | HTTPS FTP |
-Related structure data
Related structure data | 7dmxC 7dnaC 2hqkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27526.281 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-NA / | 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: 1.57 Å3/Da / Density % sol: 21.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→43.11 Å / Num. obs: 16400 / % possible obs: 92.9 % / Redundancy: 2.7 % / CC1/2: 0.997 / Net I/σ(I): 8.54 |
Reflection shell | Resolution: 2.81→2.92 Å / Num. unique obs: 2688 / CC1/2: 0.811 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HQK Resolution: 2.81→43.11 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 36.59 / 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: 92.59 Å2 / Biso mean: 38.3944 Å2 / Biso min: 1.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.81→43.11 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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