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Yorodumi- PDB-4as9: The structure of modified benzoquinone ansamycins bound to yeast ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4as9 | |||||||||
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Title | The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90 | |||||||||
Components | ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 | |||||||||
Keywords | CHAPERONE / INHIBITIOR / ANSAMYCIN | |||||||||
Function / homology | Function and homology information The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / nucleus / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | |||||||||
Authors | Roe, S.M. / Prodromou, C. | |||||||||
Citation | Journal: Nat Chem / Year: 2013 Title: Synthesis of 19-substituted geldanamycins with altered conformations and their binding to heat shock protein Hsp90. Authors: Kitson, R.R. / Chang, C.H. / Xiong, R. / Williams, H.E. / Davis, A.L. / Lewis, W. / Dehn, D.L. / Siegel, D. / Roe, S.M. / Prodromou, C. / Ross, D. / Moody, C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4as9.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4as9.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 4as9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/4as9 ftp://data.pdbj.org/pub/pdb/validation_reports/as/4as9 | 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: 24873.398 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829 |
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#2: Chemical | ChemComp-4QS / [( |
#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: 3.2 Å3/Da / Density % sol: 61.6 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→61.89 Å / Num. obs: 8868 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.71→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE MODEL Resolution: 2.71→61.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.721 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.573 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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 mean: 37.492 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→61.89 Å
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Refine LS restraints |
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