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- PDB-2i19: T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate -
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Open data
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Basic information
Entry | Database: PDB / ID: 2i19 | ||||||
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Title | T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX | ||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, R. / Mao, J. / Gao, Y. / Robinson, H. / Odeh, S. / Goddard, A. / Oldfield, E. | ||||||
![]() | ![]() Title: Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes. Authors: Mao, J. / Mukherjee, S. / Zhang, Y. / Cao, R. / Sanders, J.M. / Song, Y. / Zhang, Y. / Meints, G.A. / Gao, Y.G. / Mukkamala, D. / Hudock, M.P. / Oldfield, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 129.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 50.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ewgC ![]() 1yhkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44475.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 123.2 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2006 |
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: 2.2→30 Å / Num. all: 41878 / Num. obs: 39495 / % possible obs: 91 % / Observed criterion σ(F): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 0.101 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.424 / % possible all: 56.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YHK Resolution: 2.28→30 Å / Num. parameters: 19711 / Num. restraintsaints: 24302 / 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: 6234 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→30 Å
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Refine LS restraints |
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