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Yorodumi- PDB-2f9k: Crystal structure of human FPPS in complex with Zoledronate and Zn2+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f9k | ||||||
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Title | Crystal structure of human FPPS in complex with Zoledronate and Zn2+ | ||||||
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 / (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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.06 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 | 2f9k.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f9k.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f9k_validation.pdf.gz | 855.8 KB | Display | wwPDB validaton report |
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Full document | 2f9k_full_validation.pdf.gz | 858.8 KB | Display | |
Data in XML | 2f9k_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2f9k_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/2f9k ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f9k | HTTPS FTP |
-Related structure data
Related structure data | 2f7mC 2f89C 2f8cC 2f8zC 2f92C 2f94C 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 | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ZOL / | #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: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 0.1M zinc acetate, 0.1M sodium acetate, 12% PEG 4000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 5, 2005 |
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: 2.06→79 Å / Num. all: 27286 / Num. obs: 27286 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.23 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 8.51 / Num. unique all: 2544 / Num. unique obs: 2495 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.06→49.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2562371 / 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: 54.33 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→49.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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