+Open data
-Basic information
Entry | Database: PDB / ID: 2f7m | ||||||
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Title | Crystal Structure of Unliganded Human FPPS | ||||||
Components | Farnesyl Diphosphate Synthase | ||||||
Keywords | TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS | ||||||
Function / homology | Function and homology information geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rondeau, J.-M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. ...Rondeau, J.-M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W. | ||||||
Citation | Journal: Chemmedchem / Year: 2006 Title: Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs. Authors: Rondeau, J.M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f7m.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f7m.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 2f7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/2f7m ftp://data.pdbj.org/pub/pdb/validation_reports/f7/2f7m | HTTPS FTP |
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-Related structure data
Related structure data | 2f89C 2f8cC 2f8zC 2f92C 2f94C 2f9kC 1fpsS 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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Details | THE BIOLOGICAL ASSEMBLY IS A HOMODIMER |
-Components
#1: Protein | Mass: 40183.855 Da / Num. of mol.: 1 / Fragment: Residues 6-353 Source method: isolated from a genetically manipulated source Details: Includes: Dimethylallyltranstransferase; Geranyltranstransferase Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 TUNER(DE3) References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.2M sodium potassium phosphate, 25% glycerol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41.7 Å / Num. all: 21904 / Num. obs: 21795 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 8.17 / Num. unique all: 1851 / Num. unique obs: 1795 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FPS Resolution: 2.3→41.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2643815.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.656 Å2 / ksol: 0.388 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→41.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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