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Yorodumi- PDB-4tns: Structure of Pin1 PPIase domain bound with all-trans retinoic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tns | ||||||
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Title | Structure of Pin1 PPIase domain bound with all-trans retinoic acid | ||||||
Components | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
Keywords | ISOMERASE | ||||||
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 / negative regulation of amyloid-beta formation ...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 / negative regulation of amyloid-beta formation / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / 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 / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / tau protein binding / regulation of protein stability / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / neuron differentiation / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / cell cycle / positive regulation of protein phosphorylation / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Li, W.Z. / Zhang, Y. | ||||||
Citation | Journal: To Be Published Title: Structure of Pin1 PPIase domain bound with all-trans retinoic acid Authors: Li, W.Z. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tns.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tns.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 4tns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/4tns ftp://data.pdbj.org/pub/pdb/validation_reports/tn/4tns | HTTPS FTP |
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-Related structure data
Related structure data | 3ikgS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 51 - 162 / Label seq-ID: 39 - 150
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-Components
#1: Protein | Mass: 16636.502 Da / Num. of mol.: 2 / Fragment: UNP residues 43-163 / Mutation: K77Q, K82Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase #2: Chemical | ChemComp-REA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 24.58 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate, 0.1 M HEPES pH7-8.5 and 0.9 M-1.4 M sodium citrate PH range: 7-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→50 Å / Num. obs: 49111 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rsym value: 0.049 / Net I/σ(I): 64.9 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.465 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IKG Resolution: 1.33→42.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.805 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 14.818 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→42.34 Å
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