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Open data
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Basic information
Entry | Database: PDB / ID: 4kwv | ||||||
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Title | Crystal Structure of human apo-QPRT | ||||||
![]() | Nicotinate-nucleotide pyrophosphorylase [carboxylating] | ||||||
![]() | TRANSFERASE / NAD / metabolism / type II phosphoribosyltransferase / quinolinic acid / PRPP / brain | ||||||
Function / homology | ![]() quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / catalytic complex / extracellular exosome / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malik, S.S. / Patterson, D.N. / Ncube, Z. / Toth, E.A. | ||||||
![]() | ![]() Title: The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid. Authors: Malik, S.S. / Patterson, D.N. / Ncube, Z. / Toth, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.8 KB | Display | ![]() |
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PDB format | ![]() | 243.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.3 KB | Display | ![]() |
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Full document | ![]() | 484 KB | Display | |
Data in XML | ![]() | 54.7 KB | Display | |
Data in CIF | ![]() | 75.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kwwC ![]() 2jbmS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 2 - 286 / Label seq-ID: 6 - 290
NCS oper:
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Components
#1: Protein | Mass: 31173.826 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q15274, nicotinate-nucleotide diphosphorylase (carboxylating) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM MES, pH 6.5, 0.1 M sodium phosphate monobasic, 0.1 M potassium phosphate monobasic, 1.6-2.1 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2012 |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.797→154.7 Å / Num. all: 55406 / Num. obs: 55406 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.145 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.797→2.85 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.947 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JBM Resolution: 2.797→42.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.979 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 56.107 Å2
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Refinement step | Cycle: LAST / Resolution: 2.797→42.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3636 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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LS refinement shell | Resolution: 2.797→2.87 Å / Total num. of bins used: 20
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