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- PDB-4rzk: Crystal structure of Sulfolobus solfataricus Hsp20.1 ACD -

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Basic information

Entry
Database: PDB / ID: 4rzk
TitleCrystal structure of Sulfolobus solfataricus Hsp20.1 ACD
ComponentsSmall heat shock protein hsp20 family
KeywordsCHAPERONE
Function / homology
Function and homology information


protein complex oligomerization / response to salt stress / response to hydrogen peroxide / unfolded protein binding / protein folding / response to heat
Similarity search - Function
Heat shock protein 21-like / HSP20-like domain found in ArsA / CS domain / CS domain profile. / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like ...Heat shock protein 21-like / HSP20-like domain found in ArsA / CS domain / CS domain profile. / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Small heat shock protein hsp20 family
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.677 Å
AuthorsLiang, L. / Yun, C.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure and function of an unusual dimeric Hsp20.1 provide insight into the thermal protection mechanism of small heat shock proteins.
Authors: Liang, L. / Yun, C.H.
History
DepositionDec 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small heat shock protein hsp20 family
B: Small heat shock protein hsp20 family


Theoretical massNumber of molelcules
Total (without water)19,8852
Polymers19,8852
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.124, 91.124, 74.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Small heat shock protein hsp20 family


Mass: 9942.413 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2427 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 2% v/v tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 16% w/v polyethylene glycol 3,350, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 1, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 6449 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.65→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.677→34.915 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 300 4.65 %RANDOM
Rwork0.1932 ---
obs0.195 6449 98.8 %-
all-6455 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.677→34.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 41 1361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121330
X-RAY DIFFRACTIONf_angle_d1.2191792
X-RAY DIFFRACTIONf_dihedral_angle_d22.494514
X-RAY DIFFRACTIONf_chiral_restr0.082214
X-RAY DIFFRACTIONf_plane_restr0.008234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6769-3.37210.2921590.26193027X-RAY DIFFRACTION98
3.3721-34.9180.21921410.17293122X-RAY DIFFRACTION100

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