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Yorodumi- PDB-1y3i: Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y3i | ||||||
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Title | Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex | ||||||
Components | Inorganic polyphosphate/ATP-NAD kinase | ||||||
Keywords | TRANSFERASE / NAD kinase / polyphosphate / NAD / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information polyphosphate metabolic process / NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Mori, S. / Yamasaki, M. / Maruyama, Y. / Momma, K. / Kawai, S. / Hashimoto, W. / Mikami, B. / Murata, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2005 Title: NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex Authors: Mori, S. / Yamasaki, M. / Maruyama, Y. / Momma, K. / Kawai, S. / Hashimoto, W. / Mikami, B. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y3i.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y3i.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/1y3i ftp://data.pdbj.org/pub/pdb/validation_reports/y3/1y3i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, -y, z. |
-Components
#1: Protein | Mass: 32943.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pPnk / Plasmid: pSK27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P0A5S6, UniProt: P9WHV7*PLUS, NAD+ kinase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #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: 2.79 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate, HEPES-Na, NAD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 22375 / % possible obs: 97.5 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→10 Å / Num. parameters: 14548 / Num. restraintsaints: 19678 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3636 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.7 Å /
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