[English] 日本語
Yorodumi- PDB-5b3w: Crystal structure of hPin1 WW domain (5-15) fused with maltose-bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b3w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of hPin1 WW domain (5-15) fused with maltose-binding protein in C2221 form | |||||||||
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 transport complex / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / protein peptidyl-prolyl isomerization / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of protein dephosphorylation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / 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 regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / 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 / midbody / outer membrane-bounded periplasmic space / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / periplasmic space / protein stabilization / response to hypoxia / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5b3w.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5b3w.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 5b3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b3w_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5b3w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5b3w_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 5b3w_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/5b3w ftp://data.pdbj.org/pub/pdb/validation_reports/b3/5b3w | HTTPS FTP |
-Related structure data
Related structure data | 5b3xC 5b3yC 5b3zC 5bmyC 1anfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42054.609 Da / Num. of mol.: 2 Fragment: UNP(Q13526) residues 5-15,UNP(P0AEX9) residues 27-393 Mutation: R382N 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 #2: Polysaccharide | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 27, 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: 41976 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rsym value: 0.131 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Mean I/σ(I) obs: 3.7 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANF Resolution: 2.4→38.573 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.83
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→38.573 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|