+Open data
-Basic information
Entry | Database: PDB / ID: 5zwy | ||||||
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Title | Ribokinase from Leishmania donovani | ||||||
Components | Ribokinase | ||||||
Keywords | TRANSFERASE / Nucleotide binding / ATP binding / Metal ion binding / Ribokinase activity / Carbohydrate metabolic process / cytoplasm | ||||||
Function / homology | Function and homology information ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Gatreddi, S. / Vasudevan, D. / Qureshi, I.A. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2019 Title: Unraveling structural insights of ribokinase from Leishmania donovani. Authors: Gatreddi, S. / Pillalamarri, V. / Vasudevan, D. / Addlagatta, A. / Qureshi, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zwy.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zwy.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/5zwy ftp://data.pdbj.org/pub/pdb/validation_reports/zw/5zwy | HTTPS FTP |
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-Related structure data
Related structure data | 6a8aC 6a8bC 6a8cC 2fv7S 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: 37582.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote) Strain: BPK282A1 / Gene: LDBPK_270430 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9BIX7, ribokinase #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / #5: 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: 2.45 Å3/Da / Density % sol: 49.8 % / Description: Hexagonal |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.3 / Details: Citric acid, NaCl, Glycerol / PH range: 3.5-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9794 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2015 |
Radiation | Monochromator: Water-cooled DCM with Si (111) or Si(220) crystals Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.61 Å / Num. obs: 52575 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 0.101 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.604 / Num. unique obs: 27813 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FV7 Resolution: 1.95→46.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.569 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.137 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.197 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→46.61 Å
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