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Yorodumi- PDB-6vrx: Mucor circinelloides FKBP12 protein bound with FK506 in P3221 spa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vrx | |||||||||
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Title | Mucor circinelloides FKBP12 protein bound with FK506 in P3221 space group | |||||||||
Components | Peptidylprolyl isomerase | |||||||||
Keywords | ISOMERASE / FK506-binding protein 1A / FKBP12 / FK506 | |||||||||
Function / homology | FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / peptidylprolyl isomerase Function and homology information | |||||||||
Biological species | Mucor circinelloides (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | |||||||||
Authors | Gobeil, S. / Spicer, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mbio / Year: 2021 Title: Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs. Authors: Gobeil, S.M. / Bobay, B.G. / Juvvadi, P.R. / Cole, D.C. / Heitman, J. / Steinbach, W.J. / Venters, R.A. / Spicer, L.D. #1: Journal: Biorxiv / Year: 2020 Title: Designing Selective and Non-Immunosuppressive Antifungal FK506 Analogs: Structures, Biophysics and Dynamics of Fungal and Human Calcineurin-Inhibitor Complexes Authors: Gobeil, S.M. / Bobay, B.G. / Juvvadi, P.R. / Cole, D.C. / Heitman, J. / Steinbach, W.J. / Venters, R.A. / Spicer, L.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vrx.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vrx.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vrx_validation.pdf.gz | 607.9 KB | Display | wwPDB validaton report |
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Full document | 6vrx_full_validation.pdf.gz | 618 KB | Display | |
Data in XML | 6vrx_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 6vrx_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/6vrx ftp://data.pdbj.org/pub/pdb/validation_reports/vr/6vrx | HTTPS FTP |
-Related structure data
Related structure data | 6vctC 6vcuC 6vcvC 5huaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12095.665 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Nterminal GSH are from the expression tag / Source: (gene. exp.) Mucor circinelloides (fungus) / Gene: fkbA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U3N5X4, peptidylprolyl isomerase #2: Chemical | ChemComp-FK5 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2100 mM DL Malic acid |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→50 Å / Num. obs: 23722 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 54.87 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.043 / Rrim(I) all: 0.13 / Rsym value: 0.123 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.54→2.59 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1167 / CC1/2: 0.806 / Rpim(I) all: 0.319 / Rsym value: 0.974 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HUA Resolution: 2.54→37.2 Å / SU ML: 0.3336 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 24.329 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→37.2 Å
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Refine LS restraints |
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LS refinement shell |
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