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Open data
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Basic information
Entry | Database: PDB / ID: 3vja | ||||||
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Title | Crystal structure of the human squalene synthase | ||||||
![]() | 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. / Chang, W.J. / Wang, A.H.J. | ||||||
![]() | ![]() Title: Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase Authors: Liu, C.I. / Jeng, W.Y. / Chang, W.J. / 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 | ![]() | 303.4 KB | Display | ![]() |
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PDB format | ![]() | 245.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.3 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vj8C ![]() 3vj9C ![]() 3vjbC ![]() 3vjcC ![]() 3vjdC ![]() 3vjeC ![]() 1ezfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39448.969 Da / Num. of mol.: 2 / Fragment: UNP residues 31-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2008 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. all: 63922 / Num. obs: 62838 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.76→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.8 / Num. unique all: 6313 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EZF Resolution: 1.76→24.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.078 / SU ML: 0.089 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.133 / 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: 31.711 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→24.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.764→1.859 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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