+Open data
-Basic information
Entry | Database: PDB / ID: 1u0r | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis NAD kinase | ||||||
Components | Inorganic polyphosphate/ATP-NAD kinase | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / alpha-beta / beta sandwich / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
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 / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Garavaglia, S. / Raffaelli, N. / Finaurini, L. / Magni, G. / Rizzi, M. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: A novel fold revealed by Mycobacterium tuberculosis NAD kinase, a key allosteric enzyme in NADP biosynthesis Authors: Garavaglia, S. / Raffaelli, N. / Finaurini, L. / Magni, G. / Rizzi, M. #1: Journal: Biochemistry / Year: 2004 Title: Characterization of Mycobacterium tuberculosis NAD kinase: functional analysis of the full-length enzyme by site-directed mutagenesis Authors: Raffaelli, N. / Finaurini, L. / Mazzola, F. / Pucci, L. / Sorci, L. / Amici, A. / Magni, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0r.cif.gz | 220.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0r.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 1u0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0r ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0r | 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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-Components
#1: Protein | Mass: 32943.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ppnK / Production host: Escherichia coli (E. coli) 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: 2.5 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / pH: 5.6 Details: lithium sulfate, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793,0.9795,0.9392 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. obs: 38743 / % possible obs: 99.8 % / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.58 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.989 / ESU R Free: 0.385 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /
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