+Open data
-Basic information
Entry | Database: PDB / ID: 2f89 | ||||||
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Title | Crystal structure of human FPPS in complex with pamidronate | ||||||
Components | Farnesyl Diphosphate Synthase | ||||||
Keywords | TRANSFERASE / MEVALONATE PATHWAY / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / BISPHOSPHONATE INHIBITOR | ||||||
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: 2.6 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 | 2f89.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f89.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 2f89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/2f89 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f89 | HTTPS FTP |
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-Related structure data
Related structure data | 2f7mC 2f8cC 2f8zC 2f92C 2f94C 2f9kC C: citing same article (ref.) |
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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: Chemical | #4: Chemical | ChemComp-210 / | #5: 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: 2.57 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 1.2M Na,K phosphate, 25% glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 27, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. all: 13491 / Num. obs: 13491 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.052 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.434 / Num. unique all: 1296 / Χ2: 0.663 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→57.11 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 17969152 / 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: 58.944 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→57.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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