+Open data
-Basic information
Entry | Database: PDB / ID: 4mac | ||||||
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Title | Crystal structure of CIDE-N domain of FSP27 | ||||||
Components | Cell death activator CIDE-3 | ||||||
Keywords | APOPTOSIS / roll fold / Protein interaction / Perilipin1 | ||||||
Function / homology | Function and homology information lipid droplet fusion / Lipid particle organization / lipid transfer activity / negative regulation of triglyceride metabolic process / lipid storage / phosphatidic acid binding / lipid droplet organization / execution phase of apoptosis / phosphatidylserine binding / negative regulation of lipid catabolic process ...lipid droplet fusion / Lipid particle organization / lipid transfer activity / negative regulation of triglyceride metabolic process / lipid storage / phosphatidic acid binding / lipid droplet organization / execution phase of apoptosis / phosphatidylserine binding / negative regulation of lipid catabolic process / phosphatidylinositol binding / lipid droplet / molecular condensate scaffold activity / regulation of apoptotic process / apoptotic process / endoplasmic reticulum / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Park, H.H. / Lee, S.M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: Molecular basis for homo-dimerization of the CIDE domain revealed by the crystal structure of the CIDE-N domain of FSP27 Authors: Lee, S.M. / Jang, T.H. / Park, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mac.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mac.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mac_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 4mac_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 4mac_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 4mac_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/4mac ftp://data.pdbj.org/pub/pdb/validation_reports/ma/4mac | 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11274.087 Da / Num. of mol.: 2 / Fragment: UNP residues 32-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cidec, Fsp27 / Production host: Escherichia coli (E. coli) / References: UniProt: P56198 #2: 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: 1.93 Å3/Da / Density % sol: 36.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 28% PEG1500, MMT buffer/NaOH, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2013 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→31.68 Å / Num. all: 11299 / Num. obs: 57364 / % possible obs: 40 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.18 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.212 / 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: 33.918 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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