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Yorodumi- PDB-4a6k: Crystal structure of Slm1-PH domain in complex with D-myo-Inosito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a6k | ||||||
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Title | Crystal structure of Slm1-PH domain in complex with D-myo-Inositol-4- phosphate | ||||||
Components | PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information eisosome assembly / sphingolipid binding / establishment or maintenance of actin cytoskeleton polarity / endosomal transport / actin filament bundle assembly / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / protein localization to plasma membrane / regulation of cell growth / actin cytoskeleton organization ...eisosome assembly / sphingolipid binding / establishment or maintenance of actin cytoskeleton polarity / endosomal transport / actin filament bundle assembly / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / protein localization to plasma membrane / regulation of cell growth / actin cytoskeleton organization / mitochondrion / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Anand, K. / Maeda, K. / Gavin, A.C. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural Analyses of Slm1-Ph Domain Demonstrate Ligand Binding in the Non-Canonical Site Authors: Anand, K. / Maeda, K. / Gavin, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a6k.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a6k.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 4a6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a6k_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4a6k_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4a6k_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 4a6k_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6k ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6k | HTTPS FTP |
-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: 13777.617 Da / Num. of mol.: 4 / Fragment: PH DOMAIN, RESIDUES 469-583 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40485 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 1.98 Å3/Da / Density % sol: 37.99 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0665 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0665 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 80522 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 4.53 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.02 / % possible all: 90.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: APO STRUCTURE Resolution: 1.8→35.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.025 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.147 / 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: 22.942 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.79 Å
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