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Yorodumi- PDB-1ycd: Crystal structure of yeast FSH1/YHR049W, a member of the serine h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ycd | ||||||
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Title | Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family | ||||||
Components | Hypothetical 27.3 kDa protein in AAP1-SMF2 intergenic region | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / esterase / lipase / serine hydrolase / S. cerevisiae / Paris-Sud Yeast Structural Genomics / YSG | ||||||
Function / homology | Function and homology information carboxylic ester hydrolase activity / Hydrolases; Acting on ester bonds / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Leulliot, N. / Graille, M. / Coste, F. / Quevillon-Cheruel, S. / Janin, J. / van Tilbeurgh, H. / Paris-Sud Yeast Structural Genomics (YSG) | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family. Authors: Quevillon-Cheruel, S. / Leulliot, N. / Graille, M. / Hervouet, N. / Coste, F. / Zelwer, C. / Janin, J. / Van Tilbeurgh, H. | ||||||
History |
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Remark 600 | HETEROGEN THE AUTHOR STATES THAT THE LI5 RESIDUE IN MOLECULE B DOES NOT CONTAIN C32 ATOM BECAUSE ...HETEROGEN THE AUTHOR STATES THAT THE LI5 RESIDUE IN MOLECULE B DOES NOT CONTAIN C32 ATOM BECAUSE THIS ATOM WAS NOT DETECTED IN THE ELECTRON DENSITY FOR MOLECULE B BUT WAS DETECTED IN MOLECULE A. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ycd.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ycd.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1ycd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ycd_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 1ycd_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 1ycd_validation.xml.gz | 29 KB | Display | |
Data in CIF | 1ycd_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1ycd ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1ycd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 27342.201 Da / Num. of mol.: 2 / Fragment: S. cerevisiae YHR049wp / Mutation: F109L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YHR049w / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P38777 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 27% PEG 4K, 0.1M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 87556 / Num. obs: 57009 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.5 % / Rsym value: 0.047 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.165 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.958 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.105 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.745 Å / Total num. of bins used: 20
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