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Yorodumi- PDB-1kku: Crystal structure of nuclear human nicotinamide mononucleotide ad... -
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-Basic information
Entry | Database: PDB / ID: 1kku | ||||||
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Title | Crystal structure of nuclear human nicotinamide mononucleotide adenylyltransferase | ||||||
Components | NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / alpha/beta structure - Rossmann fold | ||||||
Function / homology | Function and homology information negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD biosynthetic process ...negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD biosynthetic process / response to wounding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / nuclear body / negative regulation of DNA-templated transcription / chromatin / nucleoplasm / ATP binding / nucleus / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Garavaglia, S. / D'Angelo, I. / Emanuelli, M. / Carnevali, F. / Pierella, F. / Magni, G. / Rizzi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure of human NMN adenylyltransferase. A key nuclear enzyme for NAD homeostasis. Authors: Garavaglia, S. / D'Angelo, I. / Emanuelli, M. / Carnevali, F. / Pierella, F. / Magni, G. / Rizzi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kku.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kku.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kku ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kku | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 32016.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: ammonium sulfate, Tris, isopropanol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2000 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 14091 / Num. obs: 14091 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 14056 / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 0.25 / Rfactor obs: 0.234 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.234 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_planar_d / Dev ideal: 0.011 |