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Yorodumi- PDB-5ael: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ael | ||||||
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Title | T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-597 | ||||||
Components | FARNESYL PYROPHOSPHATE SYNTHASEDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE | ||||||
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: 2.6 Å | ||||||
Authors | Yang, G. / Oldfield, E. / No, J.H. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2015 Title: Inhibition of Trypanosoma Brucei Cell Growth by Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation. Authors: Yang, G. / Zhu, W. / Kim, K. / Byun, S.Y. / Choi, G. / Wang, K. / Cha, J.S. / Cho, H. / Oldfield, E. / No, J.H. #1: Journal: Proteins / Year: 2008 Title: Structures of a Potent Phenylalkyl Bisphosphonate Inhibitor Bound to Farnesyl and Geranylgeranyl Diphosphate Synthases. Authors: Cao, R. / Chen, C.K. / Guo, R. / Wang, A.H. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ael.cif.gz | 158.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ael.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ael.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5ael ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5ael | HTTPS FTP |
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-Related structure data
Related structure data | 5afxC 5ahuC 2p1cS 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: 42015.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI BL21 (bacteria) References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | #3: Chemical | ChemComp-MG / #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: 2.72 Å3/Da / Density % sol: 54.76 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 6% MPD, 0.1 AMMONIUM ACETATE, PH 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→85.49 Å / Num. obs: 25663 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.61→2.66 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 16.8 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P1C Resolution: 2.6→85.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.819 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.808 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.813 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→85.49 Å
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Refine LS restraints |
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