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Yorodumi- PDB-2opm: Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2opm | ||||||
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Title | Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461 | ||||||
Components | Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)] | ||||||
Keywords | TRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Cao, R. / Gao, Y.G. / Robinson, H. / Goddard, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / ...Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / Chang, T.K. / Lin, F.Y. / Van Beek, E. / Papapoulos, S. / Wang, A.H. / Kubo, T. / Ochi, M. / Mukkamala, D. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2opm.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2opm.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 2opm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/2opm ftp://data.pdbj.org/pub/pdb/validation_reports/op/2opm | HTTPS FTP |
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-Related structure data
Related structure data | 2zeuC 2zevC 3dyfC 3dygC 3dyhC 3efqC 3egtC 1yv5S 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 on special symmetry positions |
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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, FPS, KIAA1293 / 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-NI9 / | #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: 2.33 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 10% PEG 2K, 0.5M Phosphate Citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 123.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16818 / % possible obs: 98.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.412 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1YV5 Resolution: 2.4→30 Å / Num. parameters: 11489 / Num. restraintsaints: 11300 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2868.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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