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Yorodumi- PDB-4kww: The crystal structure of human quinolinic acid phosphoribosyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kww | ||||||
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Title | The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid | ||||||
Components | Nicotinate-nucleotide pyrophosphorylase [carboxylating] | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / NAD / metabolism / type II phosphoribosyltransferase / quinolinic acid / PRPP / brain / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 2.55 Å | ||||||
Authors | Malik, S.S. / Dimeka, P.N. / Ncube, Z. / Toth, E.A. | ||||||
Citation | Journal: Proteins / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kww.cif.gz | 310 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kww.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 4kww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kww_validation.pdf.gz | 487.9 KB | Display | wwPDB validaton report |
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Full document | 4kww_full_validation.pdf.gz | 502.3 KB | Display | |
Data in XML | 4kww_validation.xml.gz | 59 KB | Display | |
Data in CIF | 4kww_validation.cif.gz | 81.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/4kww ftp://data.pdbj.org/pub/pdb/validation_reports/kw/4kww | HTTPS FTP |
-Related structure data
Related structure data | 4kwvC 2jbmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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.) Homo sapiens (human) / Gene: QPRT / Production host: Escherichia coli (E. coli) References: UniProt: Q15274, nicotinate-nucleotide diphosphorylase (carboxylating) #2: Chemical | ChemComp-PHT / #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: 3.03 Å3/Da / Density % sol: 59.39 % |
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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, 4 mM phthalic acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å |
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: 2.55→155.8 Å / Num. all: 73606 / Num. obs: 73606 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.5 % / Rsym value: 0.168 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JBM Resolution: 2.55→155.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 30.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→155.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.55→2.617 Å / Total num. of bins used: 20
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