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- PDB-1bup: T13S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1bup
TitleT13S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN
ComponentsPROTEIN (70 KILODALTON HEAT SHOCK PROTEIN)
KeywordsHYDROLASE / HYDROLASE (ACTING ON ACID ANHYDRIDES) / MOLECULAR CHAPERONE / ATPASE
Function / homologyHeat shock protein 70kD, peptide-binding domain superfamily / HSF1-dependent transactivation / Heat shock protein 70 family / Heat shock protein 70, conserved site / Heat shock protein 70kD, C-terminal domain superfamily / Hsp70 protein / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / HSP90 chaperone cycle for steroid hormone receptors (SHR) ...Heat shock protein 70kD, peptide-binding domain superfamily / HSF1-dependent transactivation / Heat shock protein 70 family / Heat shock protein 70, conserved site / Heat shock protein 70kD, C-terminal domain superfamily / Hsp70 protein / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Attenuation phase / Regulation of HSF1-mediated heat shock response / Clathrin-mediated endocytosis / mRNA Splicing - Major Pathway / Golgi Associated Vesicle Biogenesis / Protein methylation / Lysosome Vesicle Biogenesis / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / synaptic vesicle uncoating / negative regulation of supramolecular fiber organization / chaperone-mediated protein transport involved in chaperone-mediated autophagy / clathrin-uncoating ATPase activity / slow axonal transport / chaperone-mediated autophagy translocation complex disassembly / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / positive regulation by host of viral genome replication / postsynaptic specialization membrane / glycinergic synapse / C3HC4-type RING finger domain binding / chaperone complex / photoreceptor ribbon synapse / presynaptic cytosol / positive regulation of mRNA splicing, via spliceosome / regulation of postsynapse organization / Prp19 complex / axo-dendritic transport / misfolded protein binding / autophagosome / phosphatidylserine binding / protein folding chaperone / postsynaptic cytosol / ATP metabolic process / chaperone cofactor-dependent protein refolding / G protein-coupled receptor binding / ubiquitin ligase complex / spliceosomal complex / RNA splicing / vesicle-mediated transport / cellular response to unfolded protein / response to unfolded protein / heat shock protein binding / ATPase activity, coupled / regulation of cell cycle / protein binding, bridging / terminal bouton / mRNA processing / regulation of protein stability / ribonucleoprotein complex / melanosome / late endosome / unfolded protein binding / cellular response to heat / chaperone binding / lysosome / protein refolding / ATPase activity / myelin sheath / axon / glutamatergic synapse / negative regulation of transcription, DNA-templated / dendrite / nucleolus / ubiquitin protein ligase binding / perinuclear region of cytoplasm / extracellular exosome / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm / Heat shock cognate 71 kDa protein
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / OTHER / 1.7 Å resolution
AuthorsSousa, 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 3, 1998 / Release: Sep 9, 1998
RevisionDateData content typeGroupProviderType
1.0Sep 9, 1998Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (70 KILODALTON HEAT SHOCK PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1958
Polyers42,4991
Non-polymers6967
Water7,764431
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)143.572, 64.164, 46.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide PROTEIN (70 KILODALTON HEAT SHOCK PROTEIN) / HSC70


Mass: 42499.008 Da / Num. of mol.: 1 / Fragment: ATPASE FRAGMENT / Mutation: T13S / Source: (gene. exp.) Bos taurus (cattle) / Genus: Bos / Genus (production host): Escherichia / 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 / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Formula: K / Potassium
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl / Chloride
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 / Density percent sol: 50.9 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
11 mMMgATP1reservoir
250 mMCHES1reservoir
31 M1reservoirKCl
420 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Collection date: Jan 1, 1997
RadiationMonochromator: NI FILTER / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 / Relative weight: 1
ReflectionB iso Wilson estimate: 17.6 / D resolution high: 1.7 / D resolution low: 100 / Number obs: 46104 / Rsym value: 0.044 / Percent possible obs: 97.4
Reflection shellHighest resolution: 1.7 / Lowest resolution: 1.74 / Rsym value: 0.142 / Percent possible all: 90.8
Reflection
*PLUS
D resolution high: 1.7 / Number measured all: 143963 / Rmerge I obs: 0.044
Reflection shell
*PLUS
Percent possible obs: 90.8 / Rmerge I obs: 0.142

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: OTHER
Starting model: PDB ENTRY 1HPM
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 17.2 / Aniso B11: 1.53 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: -1.53 / Aniso B23: 0 / Aniso B33: 0
Least-squares processR factor R free: 0.22 / R factor R free error: 0.003 / R factor R work: 0.189 / R factor obs: 0.189 / Highest resolution: 1.7 / Lowest resolution: 1 / Number reflection R free: 4660 / Number reflection obs: 46104 / Percent reflection R free: 10.1 / Percent reflection obs: 97.2
Refine analyzeLuzzati coordinate error free: 0.21 / Luzzati coordinate error obs: 0.18 / Luzzati d res low obs: 5 / Luzzati sigma a free: 0.11 / Luzzati sigma a obs: 0.04
Refine hist #LASTHighest resolution: 1.7 / Lowest resolution: 1
Number of atoms included #LASTProtein: 2902 / Nucleic acid: 0 / Ligand: 37 / Solvent: 431 / Total: 3370
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.0
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.50
X-RAY DIFFRACTIONc_mcangle_it1.782.00
X-RAY DIFFRACTIONc_scbond_it2.352.00
X-RAY DIFFRACTIONc_scangle_it3.362.50
Refine LS shellHighest resolution: 1.7 / R factor R free: 0.267 / R factor R free error: 0.01 / R factor R work: 0.21 / Lowest resolution: 1.81 / Number reflection R free: 692 / Number reflection R work: 6528 / Total number of bins used: 6 / Percent reflection R free: 9.6 / Percent reflection obs: 92
Xplor file
Refine IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 17.2
Least-squares process
*PLUS
R factor R free: 0.22 / Highest resolution: 1.7 / Lowest resolution: 1 / Percent reflection R free: 10.1
Refine LS restraints
*PLUS
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.70
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.00
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
X-RAY DIFFRACTIONc_mcbond_it1.500
X-RAY DIFFRACTIONc_scbond_it2.000
X-RAY DIFFRACTIONc_mcangle_it2.000
X-RAY DIFFRACTIONc_scangle_it2.500
Refine LS shell
*PLUS
Highest resolution: 1.7 / Percent reflection R free: 9.6 / R factor R free: 0.267 / R factor R work: 0.21

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