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Yorodumi- PDB-4odr: Structure of SlyD delta-IF from Thermus thermophilus in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4odr | ||||||
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Title | Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506 | ||||||
Components | Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera | ||||||
Keywords | ISOMERASE / CHAPERONE / FKBP domain / peptidyl-prolyl isomerase / PPIase | ||||||
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 / regulation of amyloid precursor protein catabolic process / heart trabecula formation ...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 / regulation of amyloid precursor protein catabolic process / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / 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 / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å | ||||||
Authors | Quistgaard, E.M. / Low, C. / Nordlund, P. | ||||||
Citation | Journal: BMC Biol. / Year: 2016 Title: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD. Authors: Quistgaard, E.M. / Weininger, U. / Ural-Blimke, Y. / Modig, K. / Nordlund, P. / Akke, M. / Low, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4odr.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4odr.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4odr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4odr ftp://data.pdbj.org/pub/pdb/validation_reports/od/4odr | HTTPS FTP |
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-Related structure data
Related structure data | 4odkC 4odlC 4odmC 4odnC 4odoC 4odpC 4odqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12179.549 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria), (gene. exp.) Homo sapiens (human) Gene: TTHA0346, FKBP1, FKBP12, FKBP1A / Production host: Escherichia coli (E. coli) References: UniProt: Q5SLE7, UniProt: P62942, peptidylprolyl isomerase |
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-Non-polymers , 6 types, 327 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | PROTEIN SLYD DELTA-IF IS A CHIMERA IN WHICH THE IF DOMAIN OF SYLD (UNP RESIDUES 65-125) HAS BEEN ...PROTEIN SLYD DELTA-IF IS A CHIMERA IN WHICH THE IF DOMAIN OF SYLD (UNP RESIDUES 65-125) HAS BEEN REPLACED BY THE FLAP LOOP OF FKBP12 (UNP RESIDUES 85-97). |
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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: 4.83 Å3/Da / Density % sol: 74.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20% PEG6000, 0.1 M sodium acetate, pH 5.0, 0.2 M zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2013 |
Radiation | Monochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.929→44.5 Å / Num. all: 36885 / Num. obs: 36850 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 32.03 Å2 / Rsym value: 0.048 / Net I/σ(I): 26.72 |
Reflection shell | Resolution: 1.929→1.98 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.75 / Rsym value: 0.777 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.929→44.482 Å / SU ML: 0.18 / σ(F): 1.44 / Phase error: 15.78 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.929→44.482 Å
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Refine LS restraints |
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LS refinement shell |
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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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