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- PDB-2bup: T13G Mutant of the ATPASE fragment of Bovine HSC70 -

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Entry
Database: PDB / ID: 2bup
TitleT13G Mutant of the ATPASE fragment of Bovine HSC70
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / MOLECULAR CHAPERONE / ATPASE / HYDROLASE (ACTING ON ACID ANHYDRIDES)
Function / homologyHeat shock hsp70 proteins family signature 2. / 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 protein 70 family / Heat shock hsp70 proteins family signature 3. / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Attenuation phase ...Heat shock hsp70 proteins family signature 2. / 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 protein 70 family / Heat shock hsp70 proteins family signature 3. / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Attenuation phase / HSF1-dependent transactivation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / mRNA Splicing - Major Pathway / Clathrin-mediated endocytosis / Protein methylation / Heat shock protein 70kD, peptide-binding domain superfamily / synaptic vesicle uncoating / slow axonal transport / clathrin-uncoating ATPase activity / chaperone-mediated protein transport involved in chaperone-mediated autophagy / chaperone-mediated autophagy translocation complex disassembly / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / axo-dendritic transport / misfolded protein binding / autophagosome / protein folding chaperone / postsynaptic cytosol / chaperone cofactor-dependent protein refolding / spliceosomal complex / RNA splicing / cellular response to unfolded protein / vesicle-mediated transport / response to unfolded protein / heat shock protein binding / ATPase activity, coupled / terminal bouton / mRNA processing / ribonucleoprotein complex / melanosome / unfolded protein binding / cellular response to heat / lysosome / protein refolding / ATPase activity / axon / dendrite / negative regulation of transcription, DNA-templated / nucleolus / 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: 1995
Title: How Potassium Affects the Activity of the Molecular Chaperone Hsc70. II. Potassium Binds Specifically in the ATPase Active Site
Authors: Wilbanks, S.M. / McKay, D.B.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: How Potassium Affects the Activity of the Molecular Chaperone Hsc70. I. Potassium is Required for Optimal ATPase Activity
Authors: O'Brien, M.C. / McKay, D.B.
#3: 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.
#4: 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 8, 1998 / Release: Sep 16, 1998
RevisionDateData content typeGroupProviderType
1.0Sep 16, 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: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1549
Polyers41,9511
Non-polymers1,2038
Water7,837435
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)143.350, 64.300, 46.230
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 71 kDa protein / HSP70 / HEAT SHOCK PROTEIN / Heat shock 70 kDa protein 8


Mass: 41951.473 Da / Num. of mol.: 1 / Fragment: ATPASE / Mutation: T13G / 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 , 7 types, 443 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Formula: PO4 / Phosphate
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Formula: K / Potassium
#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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Formula: H2O / Water

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Details

Compound detailsTHE ACTIVE SITE CONTAINS A MIXTURE OF TWO GROUPS OF ATOMS. GROUP 1 IS FORMED BY ADP 486, PI 488 AND ...THE ACTIVE SITE CONTAINS A MIXTURE OF TWO GROUPS OF ATOMS. GROUP 1 IS FORMED BY ADP 486, PI 488 AND HOH 545 AND HAS AN ACCOPANCY OF 0.6. GROUP TWO IS ATP 489 AND HOH 1119 WITH AN OCCUPANCY OF 0.4

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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: 2.54 / Density percent sol: 51.55 %
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 kelvins
SourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MACSCIENCE
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 17.8 Å2 / D resolution high: 1.7 Å / D resolution low: 1 Å / Number obs: 46807 / Rmerge I obs: 0.058 / Rsym value: 0.058 / Redundancy: 4 % / Percent possible obs: 97.4
Reflection shellHighest resolution: 1.7 Å / Lowest resolution: 1.76 Å / Rsym value: 0.14 / Percent possible all: 89.5
Reflection
*PLUS
Number measured all: 167988
Reflection shell
*PLUS
Percent possible obs: 89.5 / Rmerge I obs: 0.14

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: OTHER / Details: BULK SOLVENT MODEL USED / R Free selection details: RANDOM / Data cutoff high rms absF: 1007200.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 17.1 Å2 / Aniso B11: 2.41 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -3.6 Å2 / Aniso B23: 0 Å2 / Aniso B33: 1.2 Å2
Least-squares processR factor R free: 0.224 / R factor R free error: 0.003 / R factor R work: 0.195 / R factor obs: 0.195 / Highest resolution: 1.7 Å / Lowest resolution: 3 Å / Number reflection R free: 4701 / Number reflection obs: 46807 / Percent reflection R free: 1 / Percent reflection obs: 97.5
Refine analyzeLuzzati coordinate error free: 0.22 Å / Luzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.1 Å / Luzzati sigma a obs: 0.03 Å
Refine hist #LASTHighest resolution: 1.7 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 2901 / Nucleic acid: 0 / Ligand: 68 / Solvent: 435 / Total: 3404
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.50
X-RAY DIFFRACTIONc_mcangle_it1.472.00
X-RAY DIFFRACTIONc_scbond_it1.792.00
X-RAY DIFFRACTIONc_scangle_it2.692.50
Refine LS shellHighest resolution: 1.7 Å / R factor R free: 0.264 / R factor R free error: 0.01 / R factor R work: 0.222 / Lowest resolution: 1.81 Å / Number reflection R free: 724 / Number reflection R work: 6532 / Total number of bins used: 6 / Percent reflection R free: 1 / Percent reflection obs: 92.3
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TOPPAR_MCS:BILL_DNA-RNA-ATOPPAR_MCS:ADP+PI.TOP
X-RAY DIFFRACTION3TOPPAR_MCS:ADP+PI.PARTOPPAR_MCS:BILL_ATP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 17.1 Å2
Least-squares process
*PLUS
Lowest resolution: 3 Å / Percent reflection R free: 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_deg22.80
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07
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
Percent reflection R free: 1 / R factor R free: 0.264 / R factor R work: 0.222

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