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Open data
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Basic information
Entry | Database: PDB / ID: 3o5i | ||||||
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Title | Fk1 domain of FKBP51, crystal form II | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
![]() | ISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase | ||||||
Function / homology | ![]() FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bracher, A. / Kozany, C. / Thost, A.-K. / Hausch, F. | ||||||
![]() | ![]() Title: Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90. Authors: Bracher, A. / Kozany, C. / Thost, A.K. / Hausch, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.3 KB | Display | ![]() |
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PDB format | ![]() | 88.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3o5dC ![]() 3o5eC ![]() 3o5fC ![]() 3o5gC ![]() 3o5jC ![]() 3o5kC ![]() 3o5lC ![]() 3o5mC ![]() 3o5oC ![]() 3o5pSC ![]() 3o5qC ![]() 3o5rC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13996.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 35% PEG3350, 0.2 M NH4OAc, 0.1 M HEPES, pH 7.5, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→60.193 Å / Num. all: 23588 / Num. obs: 23588 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.22 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 13.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3O5P Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2728 / WRfactor Rwork: 0.2321 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8508 / SU B: 5.269 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1632 / SU Rfree: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.139 / 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 max: 50.59 Å2 / Biso mean: 22.4799 Å2 / Biso min: 9.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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