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Yorodumi- PDB-5b3y: Crystal structure of hPin1 WW domain (5-23) fused with maltose-bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b3y | |||||||||
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Title | Crystal structure of hPin1 WW domain (5-23) fused with maltose-binding protein | |||||||||
Components | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein | |||||||||
Keywords | ISOMERASE / SUGAR BINDING PROTEIN | |||||||||
Function / homology | Function and homology information cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / detection of maltose stimulus ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / detection of maltose stimulus / negative regulation of SMAD protein signal transduction / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / synapse organization / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / neuron differentiation / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / outer membrane-bounded periplasmic space / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / periplasmic space / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / cell cycle / glutamatergic synapse / DNA damage response / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | |||||||||
Authors | Hanazono, Y. / Takeda, K. / Miki, K. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein Authors: Hanazono, Y. / Takeda, K. / Miki, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b3y.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b3y.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/5b3y ftp://data.pdbj.org/pub/pdb/validation_reports/b3/5b3y | HTTPS FTP |
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-Related structure data
Related structure data | 5b3wC 5b3xC 5b3zC 5bmyC 1anfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42949.590 Da / Num. of mol.: 1 Fragment: UNP(Q13526) residues 5-23,UNP(P0AEX9) residues 27-393 Mutation: R390N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria) Gene: PIN1, malE / Strain: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, UniProt: P0AEX9 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M Ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 27905 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rsym value: 0.084 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 6 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANF Resolution: 1.901→33.599 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→33.599 Å
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Refine LS restraints |
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LS refinement shell |
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