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Yorodumi- PDB-2xjr: X-ray structure of the N-terminal domain of the flocculin Flo5 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xjr | |||||||||
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Title | X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae in complex with calcium and Man5(D2-D3) | |||||||||
Components | FLOCCULATION PROTEIN FLO5 | |||||||||
Keywords | CELL ADHESION / GREENBEARD / PA14-DOMAIN / CARBOHYDRATE BINDING / SOCIAL INTERACTION | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 | 2xjr.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xjr.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 2xjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xjr ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xjr | HTTPS FTP |
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-Related structure data
Related structure data | 2xjpC 2xjqC 2xjsC 2xjtC 2xjuC 2xjvC 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, 2 molecules A
#1: Protein | Mass: 27732.512 Da / Num. of mol.: 1 / Fragment: LECTIN-LIKE FLO5A-DOMAIN, RESIDUES 23-271 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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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 434 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | D-MANNOSE (MAN): THESE RESIDUES CONSTITUTE |
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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: 2.77 Å3/Da / Density % sol: 55.67 % / Description: NONE |
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Crystal grow | Details: 0.5 M NACL, 0.05 M BISTRIS-PROPANE PH 7.2, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→19.43 Å / Num. obs: 85499 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED STRUCTURAL DATA Resolution: 1.25→19.35 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.963 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 197 - 199 ARE NOT WELL DEFINED. WATERS HAVE BEEN MODELLED IN THE VICINITY OF Q148 DUE TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 197 - 199 ARE NOT WELL DEFINED. WATERS HAVE BEEN MODELLED IN THE VICINITY OF Q148 DUE TO ALTERNATIVE CONFORMATIONS OF THIS RESIDUE.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.392 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→19.35 Å
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