[English] 日本語
Yorodumi- PDB-5hna: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hna | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1251 | ||||||
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: 2.693 Å | ||||||
Authors | Liu, Y.-L. / Zhang, Y. / Oldfield, E. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hna.cif.gz | 291.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hna.ent.gz | 234.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hna ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hna | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hn7C 5hn8C 5hn9C 3ldwS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43784.188 Da / Num. of mol.: 4 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-63D / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.51 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.693→50 Å / Num. obs: 46114 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 11.16 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LDW Resolution: 2.693→39.961 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 26.45
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 98.03 Å2 / Biso mean: 40.3228 Å2 / Biso min: 12.48 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.693→39.961 Å
|