+Open data
-Basic information
Entry | Database: PDB / ID: 3vj8 | ||||||
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Title | Crystal structure of the human squalene synthase | ||||||
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: 1.52 Å | ||||||
Authors | Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Wang, A.H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vj8.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vj8.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vj8_validation.pdf.gz | 420.9 KB | Display | wwPDB validaton report |
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Full document | 3vj8_full_validation.pdf.gz | 425.5 KB | Display | |
Data in XML | 3vj8_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3vj8_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/3vj8 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/3vj8 | HTTPS FTP |
-Related structure data
Related structure data | 3vj9C 3vjaC 3vjbC 3vjcC 3vjdC 3vjeC 1ezfS C: citing same article (ref.) S: Starting model for refinement |
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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: 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: 2.35 Å3/Da / Density % sol: 47.6 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 29, 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: 1.52→30 Å / Num. all: 58229 / Num. obs: 57879 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 5.4 / Num. unique all: 5755 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EZF Resolution: 1.52→23.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.174 / SU ML: 0.037 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / 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: 26.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→23.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.602 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -14.8204 Å / Origin y: -28.2264 Å / Origin z: 24.7476 Å
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Refinement TLS group |
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