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Yorodumi- PDB-2ogd: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ogd | ||||||
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Title | T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527 | ||||||
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 Å | ||||||
Authors | Cao, R. / Gao, Y. / Robinson, H. / Goddard, A. / Oldfield, E. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Bisphosphonates: Teaching Old Drugs with New Tricks Authors: Zhang, Y. / Cao, R. / Leon, A. / Guo, R.T. / Krysiak, K. / Yin, F. / Hudock, M.P. / Mukherjee, S. / Gao, Y. / Robinson, H. / Song, Y. / No, J.H. / Hong, W. / Morita, C. / Wang, A.H.-J. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ogd.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ogd.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ogd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2ogd ftp://data.pdbj.org/pub/pdb/validation_reports/og/2ogd | HTTPS FTP |
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-Related structure data
Related structure data | 2opnC 2ewgS 2ogc 2ogl 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44475.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase |
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-Non-polymers , 6 types, 580 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MPD / ( | #7: 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 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 10% MPD, 0.1 AMMONIUM ACETATE, PH 5.75, 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: X8C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 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→30 Å / Num. obs: 61155 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 0.101 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.538 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2EWG Resolution: 2→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72483.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1416 Å2 / ksol: 0.324869 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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