+Open data
-Basic information
Entry | Database: PDB / ID: 7bie | |||||||||||||||
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Title | Crystal structure of nvWrap-T, a 7-bladed symmetric propeller | |||||||||||||||
Components | nvWRAP-T | |||||||||||||||
Keywords | DE NOVO PROTEIN / synthetic construct | |||||||||||||||
Function / homology | Function and homology information microtubule organizing center organization / microtubule plus-end binding / retrograde axonal transport / microtubule associated complex / dynein complex binding / cytoplasmic microtubule / axon cytoplasm / kinetochore / neuronal cell body / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||
Authors | Lee, X.Y. / Mylemans, B. / Laier, I. / Voet, A.R.D. | |||||||||||||||
Funding support | Belgium, 4items
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Citation | Journal: Sci Rep / Year: 2021 Title: Structure and stability of the designer protein WRAP-T and its permutants. Authors: Mylemans, B. / Lee, X.Y. / Laier, I. / Helsen, C. / Voet, A.R.D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bie.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bie.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 7bie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bie_validation.pdf.gz | 380.8 KB | Display | wwPDB validaton report |
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Full document | 7bie_full_validation.pdf.gz | 382.3 KB | Display | |
Data in XML | 7bie_validation.xml.gz | 11 KB | Display | |
Data in CIF | 7bie_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/7bie ftp://data.pdbj.org/pub/pdb/validation_reports/bi/7bie | HTTPS FTP |
-Related structure data
Related structure data | 7bidC 7bifC 7bigC 2ymuS 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34346.523 Da / Num. of mol.: 2 / Mutation: No Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2J0I0 #2: Chemical | ChemComp-CIT / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.9 Å3/Da / Density % sol: 35.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Citric acid pH 4.0, 10%(w/v)PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→59.76 Å / Num. obs: 41838 / % possible obs: 98.6 % / Redundancy: 6.617 % / Biso Wilson estimate: 16.88 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Rrim(I) all: 0.099 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.225 % / Rmerge(I) obs: 0.262 / Num. unique obs: 2389 / CC1/2: 0.959 / Rrim(I) all: 0.287 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ymu Resolution: 1.8→59.76 Å / SU ML: 0.1989 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.0417 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 18.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→59.76 Å
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Refine LS restraints |
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LS refinement shell |
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