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Yorodumi- PDB-5hn7: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hn7 | ||||||
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Title | Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1158 | ||||||
Components | Farnesyl pyrophosphate synthase, putativeDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Liu, Y.-L. / Zhang, Y. / Oldfield, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Authors: G Ricci, C. / Liu, Y.L. / Zhang, Y. / Wang, Y. / Zhu, W. / Oldfield, E. / McCammon, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hn7.cif.gz | 577 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hn7.ent.gz | 474.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hn7 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hn7 | HTTPS FTP |
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-Related structure data
Related structure data | 5hn8C 5hn9C 5hnaC 3mys C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 43784.188 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Salvador I / Gene: PVX_092040 / Plasmid: P15-TEV-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K4U6 #2: Chemical | ChemComp-04M / #3: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THAT THEY HAVE DETERMINED | |
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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: 2.34 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100MM TRIS, 200MM LITHIUM SULFATE, 22% PEG 3,350, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 170179 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.6 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MYS 3mys Resolution: 2.15→36.81 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.54 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→36.81 Å
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Refine LS restraints |
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