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Yorodumi- PDB-6rn1: Structure of N-terminal truncated Plasmodium falciparum IMP-nucle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rn1 | ||||||
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Title | Structure of N-terminal truncated Plasmodium falciparum IMP-nucleotidase | ||||||
Components | IMP-specific 5'-nucleotidase, putative | ||||||
Keywords | HYDROLASE / nucleotidase / truncation | ||||||
Function / homology | Function and homology information 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 | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Carrique, L. / Ballut, L. / Violot, S. / Aghajari, N. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rn1.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rn1.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rn1_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 6rn1_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 6rn1_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 6rn1_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/6rn1 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/6rn1 | HTTPS FTP |
-Related structure data
Related structure data | 6rmdSC 6rmeC 6rmoC 6rmwC 6rnhC 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: 44947.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: First 59 residues are truncated / Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase #2: 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: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.06M citric acid, 0.04M Bis-tris propane pH 4.1 and 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 3→29.58 Å / Num. obs: 18036 / % possible obs: 99.8 % / Redundancy: 27 % / Biso Wilson estimate: 88.36 Å2 / CC1/2: 0.96 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 3→3.3 Å / Num. unique obs: 4376 / CC1/2: 0.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RMD Resolution: 3→29.578 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→29.578 Å
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Refine LS restraints |
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LS refinement shell |
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