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- PDB-3wei: Crystal structure of the human squalene synthase Y73A mutant in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wei | ||||||
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Title | Crystal structure of the human squalene synthase Y73A mutant in complex with presqualene pyrophosphate | ||||||
![]() | Squalene synthase | ||||||
![]() | TRANSFERASE / Farnesyl-diphosphate farnesyltransferase / Head-to-head synthases / Cholesterol biosynthesis / Oxidoreductase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, C.I. / Jeng, W.Y. / Wang, A.H.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.4 KB | Display | ![]() |
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PDB format | ![]() | 127.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 677.3 KB | Display | ![]() |
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Full document | ![]() | 680.3 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wefC ![]() 3wegC ![]() 3wehC ![]() 3wejC ![]() 3wekC ![]() 3vj8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39356.875 Da / Num. of mol.: 1 / Fragment: UNP residues 31-370 / Mutation: Y73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-PS7 / {( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
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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, 1mM presqualene pyrophosphate, 3mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 16, 2011 / Details: HORIZONTAL FOCUSING MIRROR |
Radiation | Monochromator: LN2-Cooled Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→30 Å / Num. all: 32256 / Num. obs: 32235 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3164 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VJ8 Resolution: 1.79→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.015 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.12 / 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: 25.748 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→30 Å
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Refine LS restraints |
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