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- PDB-1nup: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nup | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE COMPLEX WITH NMN | ||||||
![]() | FKSG76 | ||||||
![]() | TRANSFERASE / NAD BIOSYNTHESIS / MITOCHONDRIA / PYRIDINE ADENYLYLTRANSFERASE / ENZYME CATALYSIS | ||||||
Function / homology | ![]() nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / NAD biosynthetic process / response to tumor necrosis factor / response to wounding / mitochondrial matrix ...nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / NAD biosynthetic process / response to tumor necrosis factor / response to wounding / mitochondrial matrix / axon / neuronal cell body / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, X. / Kurnasov, O.V. / Karthikeyan, S. / Grishin, N.V. / Osterman, A.L. / Zhang, H. | ||||||
![]() | ![]() Title: STRUCTURAL CHARACTERIZATION OF A HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE AND IMPLICATION IN HUMAN NAD BIOSYNTHESIS Authors: ZHANG, X. / KURNASOV, O.V. / KARTHIKEYAN, S. / GRISHIN, N.V. / OSTERMAN, A.L. / ZHANG, H. #1: ![]() Title: STRUCTURE OF HUMAN NICOTINAMIDE/NICOTONIC 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.4 KB | Display | ![]() |
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PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nuqC ![]() 1nurC ![]() 1nusC ![]() 1nutC ![]() 1nuuC ![]() 1kqnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is tetramer and is genenrated by two fold axis : Y,X,-Z |
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Components
#1: Protein | Mass: 28396.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: NA CADODALYTE, LITHIUM SULPHATE, PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 6, 2003 / Details: OSMIC MIRROR |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 37796 / Num. obs: 37359 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.034 / Net I/σ(I): 49 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 8.8 / Num. unique all: 1840 / Rsym value: 0.223 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 37796 / % possible obs: 99.9 % / Num. measured all: 251859 / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.223 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KQN Resolution: 1.9→28.74 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.2717 Å2 / ksol: 0.35012 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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