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Yorodumi- PDB-1yv5: Human farnesyl diphosphate synthase complexed with Mg and risedronate -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yv5 | ||||||
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Title | Human farnesyl diphosphate synthase complexed with Mg and risedronate | ||||||
Components | Farnesyl pyrophosphate synthetase | ||||||
Keywords | TRANSFERASE / isoprenoid pathway / cholesterol synthesis / bisphosphonate / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 Å | ||||||
Authors | Kavanagh, K.L. / Guo, K. / Von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Authors: Kavanagh, K.L. / Guo, K. / Dunford, J.E. / Wu, X. / Knapp, S. / Ebetino, F.H. / Rogers, M.J. / Russell, R.G. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yv5.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yv5.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yv5 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yv5 | HTTPS FTP |
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-Related structure data
Related structure data | 1zw5C 1ubvS S: Starting model for refinement 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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-Components
#1: Protein | Mass: 43013.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS / Plasmid: pET11 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-RIS / | #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: 2.4 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 40% PEG 300, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.16 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2005 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.16 Å / Relative weight: 1 |
Reflection | Resolution: 2→70.2 Å / Num. all: 30242 / Num. obs: 30212 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4319 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UBV Resolution: 2→52.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.697 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, Restraints on magnesium to oxygen distances have been used, DENSITY NEAR THE N- AND C-TERMINI AND THE SIDE-CHAIN OF RESIDUE 34 WAS NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, Restraints on magnesium to oxygen distances have been used, DENSITY NEAR THE N- AND C-TERMINI AND THE SIDE-CHAIN OF RESIDUE 34 WAS NOT INTERPRETABLE AND WAS LEFT UNMODELLED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.087 Å2
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Refinement step | Cycle: LAST / Resolution: 2→52.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 9.7683 Å / Origin y: 30.1995 Å / Origin z: -7.1343 Å
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