+Open data
-Basic information
Entry | Database: PDB / ID: 5ayx | |||||||||
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Title | Crystal structure of Human Quinolinate Phosphoribosyltransferase | |||||||||
Components | Nicotinate-nucleotide pyrophosphorylase [carboxylating] | |||||||||
Keywords | TRANSFERASE / QUINOLINATE PHOSPHORIBOSYLTRANSFERASE / NAD BIOSYNTHESIS / NADC | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Kang, G.B. / Kim, M.-K. / Im, Y.J. / Lee, J.H. / Youn, H.-S. / An, J.Y. / Lee, J.-G. / Fukuoka, S.-I. / Eom, S.H. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis Authors: Youn, H.-S. / Kim, T.G. / Kim, M.-K. / Kang, G.B. / Kang, J.Y. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lee, Y. / Im, Y.J. / Lee, J.H. / Eom, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ayx.cif.gz | 310.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ayx.ent.gz | 254 KB | Display | PDB format |
PDBx/mmJSON format | 5ayx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ayx_validation.pdf.gz | 484.4 KB | Display | wwPDB validaton report |
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Full document | 5ayx_full_validation.pdf.gz | 522.7 KB | Display | |
Data in XML | 5ayx_validation.xml.gz | 59.8 KB | Display | |
Data in CIF | 5ayx_validation.cif.gz | 81.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayx ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayx | HTTPS FTP |
-Related structure data
Related structure data | 5ayyC 5ayzC 2jbmS S: Starting model for refinement C: citing same article (ref.) |
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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: 31946.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: QPRT / Plasmid: PET21A / Production host: Escherichia coli (E. coli) References: UniProt: Q15274, nicotinate-nucleotide diphosphorylase (carboxylating) #2: 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: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5 Details: 100MM MES-NAOH (PH 5.0), 7-15% (W/V) PEG-MME 2000, 10MM KSCN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2004 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 42775 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JBM Resolution: 2.8→48 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→48 Å
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree: 0.356 / Rfactor Rwork: 0.259 |