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- PDB-1ba1: HEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL MUTANT WIT... -

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Basic information

Entry
Database: PDB / ID: 1ba1
TitleHEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL MUTANT WITH CYS 17 REPLACED BY LYS
ComponentsHEAT-SHOCK COGNATE 70KD PROTEIN
KeywordsHYDROLASE / ACTING ON ACID ANHYDRIDES / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / presynaptic cytosol / Neutrophil degranulation / postsynaptic cytosol / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / protein folding chaperone / heat shock protein binding / RNA splicing / spliceosomal complex / ATP-dependent protein folding chaperone / terminal bouton / mRNA processing / melanosome / protein-macromolecule adaptor activity / protein refolding / lysosome / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / 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'-DIPHOSPHATE / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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.
History
DepositionApr 21, 1998Processing site: BNL
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
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)43,0846
Polymers42,5391
Non-polymers5455
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.800, 64.100, 46.100
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 , 1 types, 1 molecules A

#1: Protein HEAT-SHOCK COGNATE 70KD PROTEIN


Mass: 42539.074 Da / Num. of mol.: 1 / Fragment: 44KD ATPASE N-TERMINAL FRAGMENT / Mutation: C17K
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, EC: 3.6.1.3

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Non-polymers , 5 types, 447 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 50.73 %
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
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %ethylene glycol1reservoir
220 %PEG80001reservoir
31.0 M1reservoirNaCl
440 mMCHES1reservoir
51reservoirNaOH

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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
Highest resolution: 1.7 Å / Num. obs: 45230 / % possible obs: 94.7 % / Num. measured all: 138386 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HPM

1hpm


Resolution: 1.7→6 Å / Rfactor Rfree error: 0.6 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: SCALE ORTHORHOMBIC, LONGEST AXIS FIRST
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4454 10.1 %RANDOM
Rwork0.202 ---
obs0.202 45230 94.7 %-
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 27 9 442 3381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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: 1.7→1.76 Å / Rfactor Rfree error: 0.6 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 500 10 %
Rwork0.35 5000 -
obs--0.75 %

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