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Yorodumi- PDB-3lwt: Crystal structure of the Yeast Sac1: Implications for its phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lwt | ||||||
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Title | Crystal structure of the Yeast Sac1: Implications for its phosphoinositide phosphatase function | ||||||
Components | Phosphoinositide phosphatase SAC1 | ||||||
Keywords | HYDROLASE / sac1 / Sac3/Fig4 / phosphoinositide phosphatase / lipid metabolism / Endoplasmic reticulum / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3-phosphatase / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane / intracellular sphingolipid homeostasis / : / cortical endoplasmic reticulum ...Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3-phosphatase / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane / intracellular sphingolipid homeostasis / : / cortical endoplasmic reticulum / phosphatidylinositol dephosphorylation / Golgi medial cisterna / mitochondrial outer membrane / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.956 Å | ||||||
Authors | Mao, Y. / Manford, A. / Xia, T. / Saxena, A.K. / Stefan, C. / Hu, F. / Emr, S.D. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Crystal structure of the yeast Sac1: implications for its phosphoinositide phosphatase function. Authors: Manford, A. / Xia, T. / Saxena, A.K. / Stefan, C. / Hu, F. / Emr, S.D. / Mao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lwt.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lwt.ent.gz | 165.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lwt_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 3lwt_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 3lwt_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3lwt_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/3lwt ftp://data.pdbj.org/pub/pdb/validation_reports/lw/3lwt | 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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-Components
#1: Protein | Mass: 57741.449 Da / Num. of mol.: 1 / Fragment: Cytosolic portion of yeast Sac1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RSD1, SAC1, YKL212W / Plasmid: PETsumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P32368, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M NaCl, 0.55 M sodium Citrate, pH 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2009 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→33.2 Å / Num. all: 43960 / Num. obs: 43565 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.956→33.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.735 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.429 Å2
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Refinement step | Cycle: LAST / Resolution: 1.956→33.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.956→2.007 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.7173 Å / Origin y: 34.7116 Å / Origin z: 49.7214 Å
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