+Open data
-Basic information
Entry | Database: PDB / ID: 2dg4 | ||||||
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Title | FK506-binding protein mutant WF59 complexed with Rapamycin | ||||||
Components | FK506-binding protein 1A | ||||||
Keywords | ISOMERASE / IMMUNOPHILIN / ROTAMASE | ||||||
Function / homology | Function and homology information macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Buckle, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Energetic and structural analysis of the role of tryptophan 59 in FKBP12 Authors: Fulton, K.F. / Jackson, S.E. / Buckle, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dg4.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dg4.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dg4 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dg4 | HTTPS FTP |
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-Related 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: 11797.472 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTrcGST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62942, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-RAP / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.6 Details: 30% PEG MME 2000, 0.2M Ammonium Sulphate, pH 4.6, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 29, 2003 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.8 Å / Num. all: 12333 / Num. obs: 12333 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.7→35.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.8 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→35.58 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.061 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.111 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.221 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→35.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 Å / Total num. of bins used: 20
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