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- PDB-1ngg: STRUCTURAL BASIS OF THE 70-KILODALTON HEAT SHOCK COGNATE PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1ngg
TitleSTRUCTURAL 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
ComponentsHEAT-SHOCK COGNATE 70 kD PROTEIN
KeywordsHYDROLASE(ACTING ON ACID ANHYDRIDES)
Function / homology
Function and homology information


synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding / postsynaptic cytosol ...synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding / postsynaptic cytosol / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / cellular response to unfolded protein / heat shock protein binding / protein folding chaperone / RNA splicing / vesicle-mediated transport / spliceosomal complex / terminal bouton / mRNA processing / melanosome / unfolded protein binding / ribonucleoprotein complex / protein refolding / lysosome / dendrite / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Defensin A-like / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Defensin A-like / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.19 Å
AuthorsFlaherty, K.M. / Wilbanks, S.M. / Deluca-Flaherty, C. / Mckay, D.B.
Citation
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.
#1: 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
DepositionMay 17, 1994-
Revision 1.0Aug 31, 1994Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0173
Polymers42,4851
Non-polymers5312
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.300, 65.000, 46.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEAT-SHOCK COGNATE 70 kD PROTEIN


Mass: 42485.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: BRAIN / References: UniProt: P19120, adenosinetriphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal grow
*PLUS
pH: 9.5 / Method: unknown / Details: pH is adjusted to 9.5 with NaOH
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG800011
21.0 M11NaCl
350 mMCAPS11
41 mMMgATP11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Rmerge(I) obs: 0.035

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.19→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs0.191 14452
Refinement stepCycle: LAST / Resolution: 2.19→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 32 211 3171
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_deg1.4
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.4

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