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- PDB-5hn8: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hn8 | ||||||
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Title | Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182 | ||||||
![]() | Farnesyl pyrophosphate synthase, putative | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y.-L. / Zhang, Y. / Oldfield, E. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.5 KB | Display | ![]() |
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PDB format | ![]() | 220.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 51.5 KB | Display | |
Data in CIF | ![]() | 69.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hn7C ![]() 5hn9C ![]() 5hnaC ![]() 3ldwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 43784.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Salvador I / Gene: PVX_092040 / Production host: ![]() ![]() #2: Chemical | ChemComp-HXK / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THAT THEY HAVE DETERMINED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 200MM LISO4, 20% PEG3350, 100MM TRIS, PH 8.5, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2010 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 43920 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.561 / Rejects: 0 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LDW Resolution: 2.7→31.1 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.849 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.19 Å2 / Biso mean: 47.09 Å2 / Biso min: 6.5 Å2
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Refinement step | Cycle: final / Resolution: 2.7→31.1 Å
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Refine LS restraints |
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