+Open data
-Basic information
Entry | Database: PDB / ID: 6r5x | ||||||
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Title | 8-bladed beta-propeller formed by four 2-bladed fragments | ||||||
Components | WD-40 repeat protein | ||||||
Keywords | UNKNOWN FUNCTION / Repeat Protein / Fragment Amplification / Protein Evolution / Protein Design | ||||||
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 | Nostoc punctiforme (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Martin, J. / Lupas, A.N. / Hartmann, M.D. | ||||||
Citation | Journal: Elife / Year: 2019 Title: Structural diversity of oligomeric beta-propellers with different numbers of identical blades. Authors: Afanasieva, E. / Chaudhuri, I. / Martin, J. / Hertle, E. / Ursinus, A. / Alva, V. / Hartmann, M.D. / Lupas, A.N. #1: Journal: Elife / Year: 2019 Title: 8-bladed beta-propeller formed by four 2-bladed fragments Authors: Hartmann, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r5x.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r5x.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r5x_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 6r5x_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 6r5x_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6r5x_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/6r5x ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r5x | HTTPS FTP |
-Related structure data
Related structure data | 6r5yC 6r5zC 6r60C 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 9053.927 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R6612 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J0I0 #2: Water | ChemComp-HOH / | |
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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: 1.92 Å3/Da / Density % sol: 35.94 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium acetate 0.1 M TRIS.HCl pH 8.5 30 %(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→32.3 Å / Num. obs: 31066 / % possible obs: 99.3 % / Redundancy: 4.31 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 4842 / CC1/2: 0.861 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YMU Resolution: 1.7→32.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.769 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.908 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→32.3 Å
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Refine LS restraints |
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