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Yorodumi- PDB-4cyf: The structure of vanin-1: defining the link between metabolic dis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cyf | ||||||||||||
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Title | The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation | ||||||||||||
Components | PANTETHEINASE | ||||||||||||
Keywords | HYDROLASE / INFLAMMATION / COLITIS / COA BIOSYNTHESIS OXIDATIVE STRESS | ||||||||||||
Function / homology | Function and homology information pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / azurophil granule membrane / side of membrane / cell-cell adhesion / response to oxidative stress / inflammatory response / innate immune response / Neutrophil degranulation / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | HOMO SAPIENS (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.25 Å | ||||||||||||
Authors | Boersma, Y.L. / Newman, J. / Adams, T.E. / Sparrow, L. / Cowieson, N. / Lucent, D. / Krippner, G. / Bozaoglu, K. / Peat, T.S. | ||||||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The Structure of Vanin-1: A Key Enzyme Linking Metabolic Disease and Inflammation Authors: Boersma, Y.L. / Newman, J. / Adams, T.E. / Cowieson, N. / Krippner, G. / Bozaoglu, K. / Peat, T.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cyf.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cyf.ent.gz | 160.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cyf ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cyf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56341.219 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN, RESIDUES 22-513 Source method: isolated from a genetically manipulated source Details: FLAG TAG AT N-TERMINUS / Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHESIZED DNA / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) / References: UniProt: O95497, pantetheine hydrolase #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Sequence details | FLAG TAG AT N-TERMINUS. PRO-PEPTIDE AT C-TERMINUS HAS BEEN REMOVED IN CONSTRUCT TO GIVE THE MATURE PROTEIN | |
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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: 3.89 Å3/Da / Density % sol: 68.4 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: PROTEIN WAS AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. THE RESERVOIR WAS 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. 200 NL PLUS 200 NL DROPS IN SITTING DROP PLATES. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADXV / Detector: CCD / Date: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.3 Å / Num. obs: 77299 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.7 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 2.25→105.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.275 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. WE FIND GLYCOSYLATION AT ASN RESIDUES 38, 130, 315 AND 353 IN THIS CRYSTAL FORM. WE ALSO FIND GLYCOSYLATION ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. WE FIND GLYCOSYLATION AT ASN RESIDUES 38, 130, 315 AND 353 IN THIS CRYSTAL FORM. WE ALSO FIND GLYCOSYLATION AT POSITION 200 IN A DIFFERENT CRYSTAL FORM AND THIS IS CONFIRMED BY MASS SPEC ANALYSIS.
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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: 40.411 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→105.51 Å
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