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

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Basic information

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 / homology
Function and homology information


synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated autophagy translocation complex disassembly / chaperone-mediated protein transport involved in chaperone-mediated autophagy / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / axo-dendritic transport ...synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated autophagy translocation complex disassembly / chaperone-mediated protein transport involved in chaperone-mediated autophagy / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / axo-dendritic transport / misfolded protein binding / autophagosome / postsynaptic cytosol / chaperone cofactor-dependent protein refolding / spliceosomal complex / cellular response to unfolded protein / RNA splicing / response to unfolded protein / protein folding chaperone / vesicle-mediated transport / heat shock protein binding / ATPase activity, coupled / terminal bouton / mRNA processing / melanosome / ribonucleoprotein complex / protein refolding / unfolded protein binding / cellular response to heat / lysosome / ATPase activity / axon / dendrite / negative regulation of transcription, DNA-templated / nucleolus / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70, conserved site / Heat shock protein 70 family / Defensin A-like - #30 / Defensin A-like / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70, conserved site / Heat shock protein 70 family / Defensin A-like - #30 / Defensin A-like / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Heat shock cognate 71 kDa protein
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
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
History
DepositionApr 21, 1998-
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT-SHOCK COGNATE 70KD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1687
Polymers42,5271
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-MP212121

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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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 (DE3) / Cellular location: CYTOSOL / Organ: BRAIN / Plasmid: BL21 / 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 / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % 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
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS

Crystal-ID: 1 / Sol-ID: reservoir

IDConc.Common nameChemical formula
15 %ethylene glycol
220 %PEG8000
31.0 MNaCl
440 mMCHES
5NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 34106 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 1 / Rsym value: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 12 / Rsym value: 0.133 / % possible all: 69.7
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 102051 / 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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HPM
Resolution: 1.9→8 Å / Rfactor Rfree error: 0.6 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3357 9.8 %RANDOM
Rwork0.2161 ---
Obs0.2161 34106 88.2 %-
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 27 9 423 3367
Refine LS restraints
Refinement-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
LS refinement shellResolution: 1.9→1.94 Å / Rfactor Rfree error: 0.6 / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.312 212
Rwork0.297 1867
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 29809 / Rfactor Rfree: 0.2751

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