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- PDB-5b3x: Crystal structure of hPin1 WW domain (5-15) fused with maltose-bi... -
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Basic information
Entry | Database: PDB / ID: 5b3x | |||||||||
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Title | Crystal structure of hPin1 WW domain (5-15) fused with maltose-binding protein in P41212 form | |||||||||
![]() | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein | |||||||||
![]() | ISOMERASE / SUGAR BINDING PROTEIN | |||||||||
Function / homology | ![]() cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of SMAD protein signal transduction / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of SMAD protein signal transduction / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / detection of maltose stimulus / maltose transport complex / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / carbohydrate transport / protein peptidyl-prolyl isomerization / carbohydrate transmembrane transporter activity / maltose binding / phosphoserine residue binding / maltose transport / maltodextrin transmembrane transport / RHO GTPases Activate NADPH Oxidases / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of transforming growth factor beta receptor signaling pathway / ciliary basal body / positive regulation of GTPase activity / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein catabolic process / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / regulation of gene expression / outer membrane-bounded periplasmic space / midbody / Regulation of TP53 Activity through Phosphorylation / periplasmic space / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / DNA damage response / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hanazono, Y. / Takeda, K. / Miki, K. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 88.6 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5b3wC ![]() 5b3yC ![]() 5b3zC ![]() 5bmyC ![]() 1anfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 42054.609 Da / Num. of mol.: 1 Fragment: UNP(Q13526) residues 5-15,UNP(P0AEX9) residues 27-393 Mutation: R382N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PIN1, malE / Strain: K-12 / Production host: ![]() ![]() |
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.4→50 Å / Num. obs: 15390 / % possible obs: 100 % / Redundancy: 13.6 % / Rsym value: 0.097 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Mean I/σ(I) obs: 7.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ANF Resolution: 2.4→40.861 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1 / 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: 2.4→40.861 Å
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Refine LS restraints |
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LS refinement shell |
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