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- PDB-6rnh: Structure of C-terminal truncated Plasmodium falciparum IMP-nucle... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rnh | ||||||
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Title | Structure of C-terminal truncated Plasmodium falciparum IMP-nucleotidase | ||||||
![]() | IMP-specific 5'-nucleotidase, putative | ||||||
![]() | HYDROLASE / nucleotidase / Plasmodium falciparum | ||||||
Function / homology | ![]() nicotinamide riboside biosynthetic process / nicotinic acid riboside biosynthetic process / inosine salvage / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / IMP catabolic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carrique, L. / Ballut, L. / Violot, S. / Aghajari, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase. Authors: Carrique, L. / Ballut, L. / Shukla, A. / Varma, N. / Ravi, R. / Violot, S. / Srinivasan, B. / Ganeshappa, U.T. / Kulkarni, S. / Balaram, H. / Aghajari, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.9 KB | Display | ![]() |
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PDB format | ![]() | 154.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rmdSC ![]() 6rmeC ![]() 6rmoC ![]() 6rmwC ![]() 6rn1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50410.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: c-terminal truncated (by 10 residues) construct Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: PF3D7_1206100 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 2M ammonium sulfate, 0.1M Bis-tris pH 5.5 and 0.01M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→19.92 Å / Num. obs: 15185 / % possible obs: 99.12 % / Redundancy: 45 % / Biso Wilson estimate: 162.02 Å2 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.7→4.23 Å / Num. unique obs: 4966 / CC1/2: 0.793 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RMD Resolution: 3.7→19.92 Å / SU ML: 0.5327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2461
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 153.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→19.92 Å
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Refine LS restraints |
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LS refinement shell |
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