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- PDB-2qw9: Crystal structure of bovine hsc70 (1-394aa)in the apo state -

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Basic information

Entry
Database: PDB / ID: 2qw9
TitleCrystal structure of bovine hsc70 (1-394aa)in the apo state
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation / Stress response
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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating ...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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein folding chaperone / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / mRNA processing / melanosome / presynapse / protein-macromolecule adaptor activity / protein refolding / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / 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
Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsJiang, J. / Maes, E.G. / Wang, L. / Taylor, A.B. / Hinck, A.P. / Lafer, E.M. / Sousa, R.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis of J cochaperone binding and regulation of Hsp70.
Authors: Jiang, J. / Maes, E.G. / Taylor, A.B. / Wang, L. / Hinck, A.P. / Lafer, E.M. / Sousa, R.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
B: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9363
Polymers86,8442
Non-polymers921
Water7,440413
1
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5142
Polymers43,4221
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock cognate 71 kDa protein


Theoretical massNumber of molelcules
Total (without water)43,4221
Polymers43,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.336, 78.236, 75.462
Angle α, β, γ (deg.)90.000, 100.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8


Mass: 43422.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P19120
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 289 K / Method: microbatch under oil / pH: 8
Details: PEG3350, Calcium Acetate, pH 8.0, microbatch under oil, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 70516 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.048 / Χ2: 1.052 / Net I/σ(I): 13.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.472 / Num. unique all: 7093 / Χ2: 1.085 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.09 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.391 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3574 5.1 %RANDOM
Rwork0.202 ---
obs0.204 70503 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 6 413 6335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226015
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9588119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.145762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86124.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2181544
X-RAY DIFFRACTIONr_chiral_restr0.0880.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024524
X-RAY DIFFRACTIONr_nbd_refined0.1890.22726
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.217
X-RAY DIFFRACTIONr_mcbond_it0.6111.53919
X-RAY DIFFRACTIONr_mcangle_it0.97226096
X-RAY DIFFRACTIONr_scbond_it1.71932348
X-RAY DIFFRACTIONr_scangle_it2.7834.52023
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 272 -
Rwork0.297 4879 -
all-5151 -
obs--98.58 %

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