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Yorodumi- PDB-3vjc: Crystal structure of the human squalene synthase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vjc | ||||||
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Title | Crystal structure of the human squalene synthase in complex with zaragozic acid A | ||||||
Components | Squalene synthase | ||||||
Keywords | Transferase/Transferase inhibitor / Farnesyl-diphosphate farnesyltransferase / Head-to-head synthases / Cholesterol biosynthesis / Oxidoreductase / Transferase-Transferase inhibitor complex | ||||||
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: 1.89 Å | ||||||
Authors | Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Ko, T.P. / 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 | 3vjc.cif.gz | 875 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vjc.ent.gz | 730.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/3vjc ftp://data.pdbj.org/pub/pdb/validation_reports/vj/3vjc | HTTPS FTP |
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-Related structure data
Related structure data | 3vj8C 3vj9C 3vjaC 3vjbC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39448.969 Da / Num. of mol.: 6 / 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 #2: Chemical | ChemComp-ZGA / #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: 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: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2% PEG 400, 2M K2HPO4/NaH2PO4, 0.5mM zaragozic acid A, pH 6.5, 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 315r / Detector: CCD / Date: Jul 24, 2009 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: 1.89→30 Å / Num. all: 189042 / Num. obs: 187887 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.3 / Num. unique all: 18909 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EZF Resolution: 1.89→27.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.16 / SU ML: 0.082 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / 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: 38.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→27.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.992 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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