+Open data
-Basic information
Entry | Database: PDB / ID: 2f21 | ||||||
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Title | human Pin1 Fip mutant | ||||||
Components | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
Keywords | ISOMERASE / WW domain / beta-sheet | ||||||
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: 1.5 Å | ||||||
Authors | Jager, M. / Zhang, Y. / Bowman, M.E. / Noel, J.P. / Kelly, J.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structure-function-folding relationship in a WW domain. Authors: Jager, M. / Zhang, Y. / Bieschke, J. / Nguyen, H. / Dendle, M. / Bowman, M.E. / Noel, J.P. / Gruebele, M. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f21.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f21.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 2f21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/2f21 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/2f21 | HTTPS FTP |
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-Related structure data
Related structure data | 1zcnC 1pinS 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: 18126.127 Da / Num. of mol.: 1 / Fragment: WW domain / Mutation: R17A, S18D, S19 deletion 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 | ||
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#2: Chemical | #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: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M Ammonium Sulfate, 100mM HEPES 7.5, 0.2M NaCl. cross-seeding with wild-type Pin1 crystal, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 9 / Detector: CCD / Date: Sep 2, 2005 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. all: 27186 / Num. obs: 26346 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.043 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 2632 / Rsym value: 0.214 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PIN Resolution: 1.5→40 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati sigma a obs: 0.1 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.021
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