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Yorodumi- PDB-2xjv: X-ray structure of the N-terminal domain of the flocculin Flo5 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xjv | ||||||
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Title | X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae with mutation D201T in complex with calcium and glucose | ||||||
Components | FLOCCULATION PROTEIN FLO5 | ||||||
Keywords | CELL ADHESION / GREENBEARD / SOCIAL INTERACTION / PA14-DOMAIN / CARBOHYDRATE BINDING | ||||||
Function / homology | Function and homology information flocculation / fungal-type cell wall / cell-substrate adhesion / D-mannose binding / side of membrane / cell periphery / extracellular region Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Veelders, M. / Brueckner, S. / Ott, D. / Unverzagt, C. / Moesch, H.-U. / Essen, L.-O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Basis of Flocculin-Mediated Social Behavior in Yeast Authors: Veelders, M. / Brueckner, S. / Ott, D. / Unverzagt, C. / Moesch, H.-U. / Essen, L.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xjv.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xjv.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xjv ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xjv | HTTPS FTP |
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-Related structure data
Related structure data | 2xjpC 2xjqC 2xjrC 2xjsC 2xjtC 2xjuC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 27718.527 Da / Num. of mol.: 1 / Fragment: LECTIN-LIKE FLO5A-DOMAIN, RESIDUES 23-271 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI 2 (DE3) / References: UniProt: P38894 |
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#5: Sugar |
-Non-polymers , 4 types, 297 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | STRUCTURE CONTAINS FLO5A-DOMAIN WITH D202T MUTANT | |
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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: 2.78 Å3/Da / Density % sol: 55.82 % / Description: NONE |
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Crystal grow | Details: 0.5 M NACL, 0.1M BISTRIS-PROPANE PH7.5, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2009 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→19.42 Å / Num. obs: 32352 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED STRUCTURAL DATA Resolution: 1.74→19.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.246 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197 - 199 ARE NOT WELL DEFINED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→19.36 Å
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Refine LS restraints |
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