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Yorodumi- PDB-6rhd: Crystal structure of the amyloid-like TSYVGV segment from the Can... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rhd | ||||||
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Title | Crystal structure of the amyloid-like TSYVGV segment from the Candida albicans Agglutinin-like protein (Adhesin) 5 | ||||||
Components | Agglutinin-like protein 5 | ||||||
Keywords | PROTEIN FIBRIL / Amyloid fibril from Candida albicans | ||||||
Function / homology | Function and homology information biological process involved in symbiotic interaction / side of membrane / cell adhesion / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Model details | Adhesin | ||||||
Authors | Landau, M. / Perov, S. | ||||||
Citation | Journal: To be published Title: Amyloid structures from a Candida albicans adhesin Structure and conservation of amyloid spines from fungal adhesins Authors: Perov, S. / Landau, M. / Lipke, P.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rhd.cif.gz | 11.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rhd.ent.gz | 6.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/6rhd ftp://data.pdbj.org/pub/pdb/validation_reports/rh/6rhd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 624.684 Da / Num. of mol.: 1 Fragment: Amyloid spine segment TSYVGV from Als5 (residues 369-373) secreted by Candida albicans Source method: obtained synthetically / Details: TSYVGV from Als5, synthesized / Source: (synth.) Candida albicans (yeast) / References: UniProt: O13368 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.47 Å3/Da / Density % sol: 16.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Reservoir contained 0.1 M Na Acet 4.6 pH, 30 %v/v MPD, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 11, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→16.72 Å / Num. obs: 1178 / % possible obs: 96.2 % / Redundancy: 27.09 % / Biso Wilson estimate: 12.481 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.204 / Χ2: 0.943 / Net I/σ(I): 13.66 / Num. measured all: 31912 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→16.72 Å / Cor.coef. Fo:Fc: 0.99 / Cor.coef. Fo:Fc free: 0.987 / SU B: 1.424 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.035 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.05 Å2 / Biso mean: 8.367 Å2 / Biso min: 5.45 Å2
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Refinement step | Cycle: final / Resolution: 1.2→16.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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