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Yorodumi- PDB-2i19: T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i19 | ||||||
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Title | T. Brucei farnesyl diphosphate synthase complexed with bisphosphonate | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX | ||||||
Function / homology | Function and homology information transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Cao, R. / Mao, J. / Gao, Y. / Robinson, H. / Odeh, S. / Goddard, A. / Oldfield, E. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i19.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i19.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 2i19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/2i19 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i19 | HTTPS FTP |
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-Related structure data
Related structure data | 2ewgC 1yhkS 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: 44475.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET-28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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