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Yorodumi- PDB-1y3h: Crystal Structure of Inorganic Polyphosphate/ATP-NAD kinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y3h | ||||||
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Title | Crystal Structure of Inorganic Polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis | ||||||
Components | Inorganic polyphosphate/ATP-NAD kinase | ||||||
Keywords | TRANSFERASE / NAD kinase / polyphosphate / NAD / ATP | ||||||
Function / homology | Function and homology information NAD+ kinase / polyphosphate metabolic process / 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 / MIR / Resolution: 2.8 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 | 1y3h.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y3h.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1y3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/1y3h ftp://data.pdbj.org/pub/pdb/validation_reports/y3/1y3h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a tetramer |
-Components
#1: Protein | Mass: 32955.711 Da / Num. of mol.: 2 / Mutation: T302I 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: 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: 3 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, Sodium 2-morpholinoethanesulfonic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 34670 / Num. obs: 18419 / % possible obs: 91.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 51.5 Å2 / Rsym value: 0.063 |
Reflection shell | Resolution: 2.8→2.89 Å / % possible all: 78.39 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→9.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1056320.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.4984 Å2 / ksol: 0.312612 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→9.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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