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- PDB-1ba0: HEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL 1NGE 3 -

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Entry
Database: PDB / ID: 1ba0
TitleHEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL 1NGE 3
ComponentsHEAT-SHOCK COGNATE 70KD PROTEIN
KeywordsHYDROLASE / ACTING ON ACID ANHYDRIDES / ATP-BINDING / HEAT SHOCK
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 / positive regulation of mRNA splicing, via spliceosome / presynaptic cytosol / regulation of postsynapse organization / Prp19 complex / axo-dendritic transport / misfolded protein binding / phosphatidylserine binding / autophagosome / 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 / cellular response to unfolded protein / vesicle-mediated transport / 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 / dendrite / negative regulation of transcription, DNA-templated / 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 / MOLECULAR REPLACEMENT / 1.9 Å resolution
AuthorsWilbanks, S.M. / Mckay, D.B.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural replacement of active site monovalent cations by the epsilon-amino group of lysine in the ATPase fragment of bovine Hsc70.
Authors: Wilbanks, S.M. / McKay, D.B.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Structural Basis of the 70-Kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity. II. Structure of the Active Site with Adp or ATP Bound to Wild Type and Mutant ATPase Fragment
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: Apr 21, 1998 / Release: Jul 15, 1998
RevisionDateData content typeGroupProviderType
1.0Jul 15, 1998Structure modelrepositoryInitial release
1.1Mar 24, 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: HEAT-SHOCK COGNATE 70KD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1687
Polyers42,5271
Non-polymers6406
Water7,620423
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)143.300, 63.800, 46.500
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 HEAT-SHOCK COGNATE 70KD PROTEIN


Mass: 42527.129 Da / Num. of mol.: 1 / Fragment: 44KD ATPASE N-TERMINAL FRAGMENT / Mutation: D206K / Source: (gene. exp.) Bos taurus (cattle) / Genus: Bos / Cell line: BL21 (DE3) / Cellular location: CYTOSOL / Organ: BRAIN / Plasmid name: BL21 / Genus (production host): Escherichia / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P19120, adenosinetriphosphatase

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Non-polymers , 6 types, 429 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl / Chloride
#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.: 423 / 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: 50.77 %
Crystal growpH: 9
Details: 20% PEG-8000 1.0M NACL 50MM CHES, PH 9 1MM MGATP, pH 9.0
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: used to seeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
15 %ethylene glycol1reservoir
220 %PEG80001reservoir
31.0 M1reservoirNaCl
440 mMCHES1reservoir
51reservoirNaOH

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Collection date: Oct 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 40 Å / Number obs: 34106 / Observed criterion sigma I: 3 / Rmerge I obs: 1 / Rsym value: 0.056 / NetI over sigmaI: 16 / Redundancy: 3.2 % / Percent possible obs: 99
Reflection shellRmerge I obs: 1 / Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / MeanI over sigI obs: 12 / Rsym value: 0.133 / Redundancy: 1.2 % / Percent possible all: 69.7
Reflection
*PLUS
Number measured all: 102051 / Percent possible obs: 99 / Rmerge I obs: 0.056

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HPM
R Free selection details: RANDOM / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / Sigma F: 2
Least-squares processR factor R free: 0.275 / R factor R free error: 0.6 / R factor R work: 0.2161 / R factor obs: 0.2161 / Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Number reflection R free: 3357 / Number reflection obs: 34106 / Percent reflection R free: 9.8 / Percent reflection obs: 88.2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 4 Å
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 2908 / Nucleic acid: 27 / Ligand: 9 / Solvent: 423 / Total: 3367
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS shellHighest resolution: 1.9 Å / R factor R free: 0.312 / R factor R free error: 0.6 / R factor R work: 0.297 / Lowest resolution: 1.94 Å / Number reflection R free: 212 / Number reflection R work: 1867 / Total number of bins used: 15
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.2751 / Number reflection obs: 29809

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