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- PDB-8s7a: HSPB8acd-C99S/F155T/A156S -

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Basic information

Entry
Database: PDB / ID: 8s7a
TitleHSPB8acd-C99S/F155T/A156S
ComponentsHeat shock protein beta-8
KeywordsCHAPERONE / apo
Function / homology
Function and homology information


positive regulation of aggrephagy / protein folding chaperone complex / cellular response to unfolded protein / HSF1-dependent transactivation / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Heat shock protein beta-8, alpha-crystallin domain (ACD) / Heat shock protein beta-8 / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Heat shock protein beta-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsWang, Z. / Benesch, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: HSPB8acd C99S/F155T/A156S
Authors: Wang, Z. / Benesch, J.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3293
Polymers9,1401
Non-polymers1882
Water23413
1
A: Heat shock protein beta-8
hetero molecules

A: Heat shock protein beta-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6576
Polymers18,2812
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area2420 Å2
ΔGint-49 kcal/mol
Surface area9330 Å2
Unit cell
Length a, b, c (Å)98.273, 98.273, 42.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Heat shock protein beta-8 / HspB8 / Alpha-crystallin C chain / E2-induced gene 1 protein / Protein kinase H11 / Small stress ...HspB8 / Alpha-crystallin C chain / E2-induced gene 1 protein / Protein kinase H11 / Small stress protein-like protein HSP22


Mass: 9140.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB8, CRYAC, E2IG1, HSP22, PP1629 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UJY1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate monohydrate 0.1 M Tris pH 8.5 1.26 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2022
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→34.745 Å / Num. obs: 7957 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.6
Reflection shellResolution: 1.95→5.29 Å / Redundancy: 13.6 % / Rmerge(I) obs: 4.188 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 389 / CC1/2: 0.285 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→34.745 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 371 4.68 %
Rwork0.2284 --
obs0.2301 7925 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.951→34.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms575 0 11 13 599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004623
X-RAY DIFFRACTIONf_angle_d0.707842
X-RAY DIFFRACTIONf_dihedral_angle_d2.215523
X-RAY DIFFRACTIONf_chiral_restr0.04795
X-RAY DIFFRACTIONf_plane_restr0.004107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.951-2.23270.38191100.37992465X-RAY DIFFRACTION99
2.2327-2.81280.33831310.3342478X-RAY DIFFRACTION100
2.8128-34.7450.24191300.19922611X-RAY DIFFRACTION100

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