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Yorodumi- PDB-1kr2: CRYSTAL STRUCTURE OF HUMAN NMN/NAMN ADENYLYL TRANSFERASE COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kr2 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN NMN/NAMN ADENYLYL TRANSFERASE COMPLEXED WITH TIAZOFURIN ADENINE DINUCLEOTIDE (TAD) | ||||||
Components | NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE | ||||||
Keywords | TRANSFERASE / nucleotidyltransferase superfamily | ||||||
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 / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure of Hhuman of Nicotinamide/Nicotinic Acid Mononucleotide Adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. Authors: Zhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kr2.cif.gz | 303.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kr2.ent.gz | 247.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kr2_validation.pdf.gz | 819.4 KB | Display | wwPDB validaton report |
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Full document | 1kr2_full_validation.pdf.gz | 856.1 KB | Display | |
Data in XML | 1kr2_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 1kr2_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1kr2 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1kr2 | HTTPS FTP |
-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: 31982.502 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase #2: Chemical | ChemComp-TAD / #3: 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: 3.74 Å3/Da / Density % sol: 67.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 2, 2001 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 132752 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.7 |
Reflection | *PLUS Highest resolution: 2.25 Å / Num. measured all: 453541 |
Reflection shell | *PLUS % possible obs: 85.5 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KR2 Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.204 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.014 |