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- PDB-4yub: Crystal structure of human Nicotinic Acid Phosphoribosyltransferase -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yub | ||||||
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Title | Crystal structure of human Nicotinic Acid Phosphoribosyltransferase | ||||||
![]() | Nicotinate phosphoribosyltransferase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garavaglia, S. / Rizzi, M. / Marletta, A.S. | ||||||
![]() | ![]() Title: Crystal structure of human nicotinic acid phosphoribosyltransferase. Authors: Marletta, A.S. / Massarotti, A. / Orsomando, G. / Magni, G. / Rizzi, M. / Garavaglia, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.5 KB | Display | ![]() |
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PDB format | ![]() | 159.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2f7fS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 57628.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q6XQN6, ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Sodium cacodylate pH 6.5 and 1.7 M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→58.64 Å / Num. obs: 25261 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 10 |
Reflection shell | Highest resolution: 2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2F7F Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 18.062 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.616 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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