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- PDB-2f8z: Crystal structure of human FPPS in complex with zoledronate and i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f8z | ||||||
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Title | Crystal structure of human FPPS in complex with zoledronate and isopentenyl diphosphate | ||||||
![]() | Farnesyl Diphosphate Synthase | ||||||
![]() | TRANSFERASE / Mevalonate pathway / isoprene biosynthesis / cholesterol biosynthesis / bisphosphonate inhibitor | ||||||
Function / homology | ![]() geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.6 KB | Display | ![]() |
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Full document | ![]() | 813.9 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f7mC ![]() 2f89C ![]() 2f8cSC ![]() 2f92C ![]() 2f94C ![]() 2f9kC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 |
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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.) ![]() ![]() ![]() References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IPE / | #4: Chemical | ChemComp-ZOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % |
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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 292K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00033 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.035 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.481 / Num. unique all: 1282 / Χ2: 0.649 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F8C Resolution: 2.6→56.71 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 18221610 / 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: 55.171 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→56.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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