+Open data
-Basic information
Entry | Database: PDB / ID: 1ezf | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN SQUALENE SYNTHASE | ||||||
Components | FARNESYL-DIPHOSPHATE FARNESYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / isoprenoid synthase fold / all alpha-helix | ||||||
Function / homology | Function and homology information farnesyl diphosphate metabolic process / squalene synthase / farnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / Cholesterol biosynthesis / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane ...farnesyl diphosphate metabolic process / squalene synthase / farnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / Cholesterol biosynthesis / steroid 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 / MIRAS / Resolution: 2.15 Å | ||||||
Authors | Pandit, J. / Danley, D.E. / Schulte, G.K. / Mazzalupo, S.M. / Pauly, T.A. / Hayward, C.M. / Hamanaka, E.S. / Thompson, J.F. / Harwood, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis. Authors: Pandit, J. / Danley, D.E. / Schulte, G.K. / Mazzalupo, S. / Pauly, T.A. / Hayward, C.M. / Hamanaka, E.S. / Thompson, J.F. / Harwood Jr., H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ezf.cif.gz | 210.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ezf.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ezf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/1ezf ftp://data.pdbj.org/pub/pdb/validation_reports/ez/1ezf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 39221.805 Da / Num. of mol.: 3 / Fragment: RESIDUES 31-370 / Mutation: Q33R, D34N, S38N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHSS9 / Production host: Escherichia coli (E. coli) / References: UniProt: P37268, squalene synthase #2: Chemical | #3: 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: 2.32 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25-30% PEG 4000, 0.1M sodium citrate, pH5.6, 0.2M ammonium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1995 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Observed criterion σ(I): -3 / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 7.2 / % possible all: 84.9 |
Reflection | *PLUS Num. obs: 55224 / % possible obs: 96 % |
Reflection shell | *PLUS % possible obs: 84.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.15→40 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Cross valid method: Free-R / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.15→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Total num. of bins used: 10
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