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Yorodumi- PDB-5j1b: structure of the core domaine of Knr4, an intrinsically disordere... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j1b | ||||||
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Title | structure of the core domaine of Knr4, an intrinsically disordered protein from Saccharomyces cerevisiae - WT. | ||||||
Components | Cell wall assembly regulator SMI1 | ||||||
Keywords | SIGNALING PROTEIN / cell-wall integrity / stress response / beta-glucan synthesis | ||||||
Function / homology | Function and homology information regulation of fungal-type cell wall biogenesis / fungal-type cell wall beta-glucan biosynthetic process / incipient cellular bud site / cellular bud neck / mating projection tip / regulation of mitotic cell cycle / cell wall organization / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Maveyraud, L. / Batista, M. / Martin-yken, H. / Francois, J.M. / Zerbib, D. / Mourey, L. | ||||||
Citation | Journal: To Be Published Title: Structural and biophysical characterization of Knr4, an intrinsically disordered hub protein form Saccharomyces cerevisiae Authors: Batista, M. / Maveyraud, L. / Zerbib, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j1b.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j1b.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 5j1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j1b_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 5j1b_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 5j1b_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5j1b_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j1b ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j1b | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30921.141 Da / Num. of mol.: 2 / Fragment: UNP residues 80-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SMI1, KNR4, KTR4, YGR229C, G8553 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32566 |
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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: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG (3000-6000) 15 - 24 % (w/v) pH 8.0 - 9.0 / PH range: 8.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40.25 Å / Num. obs: 19048 / % possible obs: 99.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 82 Å2 / CC1/2: 0.999 / Rsym value: 0.04 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 29.377 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.129 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→35 Å
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