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

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Basic information

Entry
Database: PDB / ID: 2qwl
TitleCrystal structure of bovine hsc70 (1-394aa)in the ADP state
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation / Stress response
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'-DIPHOSPHATE / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)87,93111
Polymers86,8442
Non-polymers1,0879
Water14,430801
1
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9205
Polymers43,4221
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0126
Polymers43,4221
Non-polymers5905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.306, 77.962, 75.320
Angle α, β, γ (deg.)90.000, 101.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 810 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
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

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 83895 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.033 / Χ2: 1.045 / Net I/σ(I): 26.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.50.23482941.071100
1.81-1.893.50.17483971.0651100
1.89-1.973.50.12283161.0411100
1.97-2.073.60.08683591.0351100
2.07-2.23.60.06483661.0951100
2.2-2.383.60.04983661.0261100
2.38-2.613.70.03884421.0721100
2.61-2.993.70.02883601.0031100
2.99-3.773.70.02184511.0291100
3.77-503.70.01885441.019199.9

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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
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→35.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.9 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4182 5 %RANDOM
Rwork0.176 ---
obs0.177 83752 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.947 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 66 801 6765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226055
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9698187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0235760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55524.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.274151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9481544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024538
X-RAY DIFFRACTIONr_nbd_refined0.1950.22922
X-RAY DIFFRACTIONr_nbtor_refined0.30.24237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2589
X-RAY DIFFRACTIONr_metal_ion_refined0.130.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.245
X-RAY DIFFRACTIONr_mcbond_it0.5531.53774
X-RAY DIFFRACTIONr_mcangle_it1.01226080
X-RAY DIFFRACTIONr_scbond_it2.06932319
X-RAY DIFFRACTIONr_scangle_it3.3884.52107
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 293 -
Rwork0.259 5822 -
all-6115 -
obs--99.87 %

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