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Yorodumi- PDB-3weg: Crystal structure of the human squalene synthase in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3weg | ||||||
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Title | Crystal structure of the human squalene synthase in complex with farnesyl thiopyrophosphate and magnesium ion | ||||||
Components | Squalene synthase | ||||||
Keywords | TRANSFERASE / Farnesyl-diphosphate farnesyltransferase / Head-to-head synthases / Cholesterol biosynthesis / Oxidoreductase | ||||||
Function / homology | Function and homology information squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) ...squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / ergosterol biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Liu, C.I. / Jeng, W.Y. / Wang, A.H.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural insights into the catalytic mechanism of human squalene synthase. Authors: Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Shih, M.F. / Ko, T.P. / Wang, A.H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3weg.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3weg.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 3weg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3weg_validation.pdf.gz | 853.1 KB | Display | wwPDB validaton report |
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Full document | 3weg_full_validation.pdf.gz | 855.6 KB | Display | |
Data in XML | 3weg_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3weg_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/3weg ftp://data.pdbj.org/pub/pdb/validation_reports/we/3weg | HTTPS FTP |
-Related structure data
Related structure data | 3wefC 3wehC 3weiC 3wejC 3wekC 3vj8S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 39448.969 Da / Num. of mol.: 1 / Fragment: UNP residues 31-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P37268, squalene synthase | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 4000, 10% 2-propanol, 0.1M HEPES, 3mM farnesyl thiopyrophosphate, 1mM MgCl2, 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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2010 / Details: mirrors |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 35232 / Num. obs: 34977 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3427 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VJ8 Resolution: 1.75→28.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.881 / SU ML: 0.071 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.112 / 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: 25.516 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→28.43 Å
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