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- PDB-2xjp: X-ray structure of the N-terminal domain of the flocculin Flo5 fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xjp | ||||||
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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 mannose | ||||||
![]() | FLOCCULATION PROTEIN FLO5 | ||||||
![]() | CELL ADHESION / GREENBEARD / PA14-DOMAIN / CARBOHYDRATE BINDING / SOCIAL INTERACTION | ||||||
Function / homology | ![]() flocculation / fungal-type cell wall / cell-substrate adhesion / D-mannose binding / side of membrane / cell periphery / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Veelders, M. / Brueckner, S. / Ott, D. / Unverzagt, C. / Moesch, H.-U. / Essen, L.-O. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.7 KB | Display | ![]() |
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PDB format | ![]() | 200.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.4 KB | Display | ![]() |
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Full document | ![]() | 481.9 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xjqC ![]() 2xjrC ![]() 2xjsC ![]() 2xjtC ![]() 2xjuC ![]() 2xjvC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 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.) ![]() ![]() Strain: S288C / Production host: ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/BMA.gif)
#5: Sugar | ChemComp-MAN / |
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#6: Sugar |
-Non-polymers , 4 types, 465 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | D-MANNOSE(MAN): MANNOSE HAS BEEN FOUND IN BOTH ANOMERIC CONFORMATION AS ACCOUNTED BY THE ...D-MANNOSE(MAN): MANNOSE HAS BEEN FOUND IN BOTH ANOMERIC CONFORMATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % / Description: NONE |
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Crystal grow | Details: 0.5 M NACL, 0.1 M BISTRIS PH7.5, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2008 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR |
Radiation | Monochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9149 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→40.29 Å / Num. obs: 190329 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 0.95→1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 0.95→20 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.375 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197 - 199 ARE NOT WELL DEFINED. RESIDUES 200 - 204 HAVE BEEN MODELLED IN TWO DISTINCT CONFORMATIONS.
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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: 12.246 Å2
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Refinement step | Cycle: LAST / Resolution: 0.95→20 Å
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Refine LS restraints |
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