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Yorodumi- PDB-1bgq: RADICICOL BOUND TO THE ATP BINDING SITE OF THE N-TERMINAL DOMAIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bgq | ||||||
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Title | RADICICOL BOUND TO THE ATP BINDING SITE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE | ||||||
Components | HEAT SHOCK PROTEIN 90 | ||||||
Keywords | CHAPERONE / ATP-BINDING / HEAT SHOCK / INHIBITOR | ||||||
Function / homology | Function and homology information The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / 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 / response to osmotic stress / regulation of telomere maintenance / 'de novo' protein folding / protein maturation / proteasome assembly / Neutrophil degranulation / positive regulation of telomere maintenance via telomerase / 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 / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Roe, S.M. / Prodromou, C. / Pearl, L.H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1999 Title: Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin. Authors: Roe, S.M. / Prodromou, C. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Identification and Structural Characterization of the ATP/Adp-Binding Site in the Hsp90 Molecular Chaperone Authors: Prodromou, C. / Roe, S.M. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H. #2: Journal: Proteins / Year: 1996 Title: Expression and Crystallization of the Yeast Hsp82 Chaperone, and Preliminary X-Ray Diffraction Studies of the Amino-Terminal Domain Authors: Prodromou, C. / Piper, P.W. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bgq.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bgq.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bgq_validation.pdf.gz | 859.4 KB | Display | wwPDB validaton report |
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Full document | 1bgq_full_validation.pdf.gz | 862.9 KB | Display | |
Data in XML | 1bgq_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1bgq_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bgq ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bgq | HTTPS FTP |
-Related structure data
Related structure data | 1ah6S S: Starting model for refinement |
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Similar 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: 25527.037 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cell line: BL21 / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P02829 |
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#2: Chemical | ChemComp-RDC / |
#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: 2.97 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MSC MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 11672 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.073 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.46→2.58 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.233 / % possible all: 99.1 |
Reflection | *PLUS Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.233 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: 1AH6 Resolution: 2.5→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 24.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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