+Open data
-Basic information
Entry | Database: PDB / ID: 2w61 | ||||||
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Title | Saccharomyces cerevisiae Gas2p apostructure (E176Q mutant) | ||||||
Components | GLYCOLIPID-ANCHORED SURFACE PROTEIN 2 | ||||||
Keywords | GLYCOPROTEIN / CELL MEMBRANE / FUNGAL CELL WALL / TRANSGLYCOSYLATION / GLUCAN / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN | ||||||
Function / homology | Function and homology information 1,3-beta-glucanosyltransferase activity / fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process / ascospore wall assembly / fungal-type cell wall organization / fungal-type vacuole / Transferases; Glycosyltransferases; Hexosyltransferases / side of membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Schuettelkopf, A.W. / Hurtado-Guerrero, R. / van Aalten, D.M.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Molecular Mechanisms of Yeast Cell Wall Glucan Remodeling. Authors: Hurtado-Guerrero, R. / Schuttelkopf, A.W. / Mouyna, I. / Ibrahim, A.F.M. / Shepherd, S. / Fontaine, T. / Latge, J. / Van Aalten, D.M.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w61.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w61.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w61 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w61 | 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 | Mass: 62425.016 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: W303 / Plasmid: PPICZALPHA-BASED / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33 References: UniProt: Q06135, Transferases; Glycosyltransferases; Hexosyltransferases | ||
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#2: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | E176Q POINT MUTANT, MISSING RESIDUES WERE NOT MODELLED DUE TO LACKING ELECTRON DENSITY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Details: 100 MM SODIUM ACETATE PH 4.5; 5% ACETONE; 20% 1,4-BUTANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→20 Å / Num. obs: 64209 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.12 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DERIVATIVE MODEL, NOT DEPOSITED Resolution: 1.62→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.089 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.094 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→25 Å
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Refine LS restraints |
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