+Open data
-Basic information
Entry | Database: PDB / ID: 1bup | ||||||
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Title | T13S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN | ||||||
Components | PROTEIN (70 KILODALTON HEAT SHOCK PROTEIN) | ||||||
Keywords | HYDROLASE / HYDROLASE (ACTING ON ACID ANHYDRIDES) / MOLECULAR CHAPERONE / ATPASE | ||||||
Function / homology | Function and homology information Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / mRNA processing / melanosome / presynapse / protein-macromolecule adaptor activity / protein refolding / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.7 Å | ||||||
Authors | Sousa, M.C. / Mckay, D.B. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change. Authors: Sousa, M.C. / McKay, D.B. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Structural Basis of the 70-Kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity Authors: Flaherty, K.M. / Wilbanks, S.M. / Deluca-Flaherty, C. / Mckay, D.B. #2: Journal: Nature / Year: 1990 Title: Three-Dimensional Structure of the ATPase Fragment of a 70K Heat-Shock Cognate Protein Authors: Flaherty, K.M. / Deluca-Flaherty, C. / Mckay, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bup.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bup.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bup_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 1bup_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 1bup_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1bup_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1bup ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1bup | HTTPS FTP |
-Related structure data
Related structure data | 2bupC 1hpmS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42499.008 Da / Num. of mol.: 1 / Fragment: ATPASE FRAGMENT / Mutation: T13S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19120 |
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-Non-polymers , 6 types, 438 molecules
#2: Chemical | ChemComp-MG / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-ADP / | #7: 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: 2.5 Å3/Da / Density % sol: 50.9 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 46104 / % possible obs: 97.4 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.044 |
Reflection shell | Resolution: 1.7→1.74 Å / Rsym value: 0.142 / % possible all: 90.8 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. measured all: 143963 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 90.8 % / Rmerge(I) obs: 0.142 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1HPM Resolution: 1.7→100 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Rfactor Rfree: 0.267 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.21 |