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Yorodumi- PDB-3n4w: Crystal structure of an abridged SER to ALA mutant of the mature ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n4w | ||||||
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Title | Crystal structure of an abridged SER to ALA mutant of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase ICA512/IA-2 at pH 7.5 | ||||||
Components | Receptor-type tyrosine-protein phosphatase-like N | ||||||
Keywords | TRANSFERASE / IA-2 / ICA-512 / PROTEIN-TYROSINE PHOSPHATASE / TRANSMEMBRANE PROTEIN / DIABETES / AUTOIMMUNITY / PROTEOLYSIS / GLYCOPROTEIN / RECEPTOR | ||||||
Function / homology | Function and homology information dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / spectrin binding / transport vesicle membrane / transcription factor binding / ubiquitin-like protein ligase binding ...dense core granule maturation / positive regulation of type B pancreatic cell proliferation / regulation of secretion / luteinization / insulin secretion involved in cellular response to glucose stimulus / insulin secretion / spectrin binding / transport vesicle membrane / transcription factor binding / ubiquitin-like protein ligase binding / axon terminus / secretory granule / response to reactive oxygen species / perikaryon / endosome / neuronal cell body / synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Primo, M.E. / Jakoncic, J. / Poskus, E. / Ermacora, M.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2. Authors: Primo, M.E. / Klinke, S. / Sica, M.P. / Goldbaum, F.A. / Jakoncic, J. / Poskus, E. / Ermacora, M.R. #1: Journal: J.Biol.Chem. / Year: 2008 Title: Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2 Authors: Primo, M.E. / Klinke, S. / Sica, M.P. / Goldbaum, F.A. / Jakoncic, J. / Poskus, E. / Ermacora, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n4w.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n4w.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3n4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n4w_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 3n4w_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 3n4w_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3n4w_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4w ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4w | HTTPS FTP |
-Related structure data
Related structure data | 2qt7SC 3ng8C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9621.916 Da / Num. of mol.: 2 / Fragment: UNP residues 470-558 / Mutation: S508A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ICA3, ICA512, PTPRN / Plasmid: PET9B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q16849 #2: Chemical | ChemComp-CA / | #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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% (W/V) PEG 4000, 0.1 M HEPES PH 7.5, 0.2 M CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 14, 2010 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI (111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. obs: 27641 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 51.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1314 / Rsym value: 0.407 / % possible all: 95.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QT7 Resolution: 1.45→19.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.524 / SU ML: 0.045 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.08 / Stereochemistry target values: Engh & Huber / Details: U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40 Å2 / Biso mean: 22.751 Å2 / Biso min: 12.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→19.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Total num. of bins used: 20
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