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- PDB-4ylb: Crystal Structure of A102D mutant of hsp14.1 from Sulfolobus solf... -

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Basic information

Entry
Database: PDB / ID: 4ylb
TitleCrystal Structure of A102D mutant of hsp14.1 from Sulfolobus solfatataricus P2
ComponentsHeat shock protein Hsp20
KeywordsCHAPERONE / Small heat shock protein / Molecular chaperone / SsHsp14.1
Function / homology
Function and homology information


metal ion binding / identical protein binding
Similarity search - Function
HSP20-like domain found in ArsA / : / 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
Heat shock protein Hsp20
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.501 Å
AuthorsLiu, L. / Chen, J.Y. / Yun, C.H.
CitationJournal: Structure / Year: 2015
Title: Active-State Structures of a Small Heat-Shock Protein Revealed a Molecular Switch for Chaperone Function
Authors: Liu, L. / Chen, J.Y. / Yang, B. / Wang, F.H. / Wang, Y.H. / Yun, C.H.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein Hsp20
B: Heat shock protein Hsp20
C: Heat shock protein Hsp20
D: Heat shock protein Hsp20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1907
Polymers58,0834
Non-polymers1063
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-86 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.793, 132.793, 213.058
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Heat shock protein Hsp20 / Small heat shock protein 14.1


Mass: 14520.835 Da / Num. of mol.: 4 / Mutation: A102D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain 98/2) (archaea)
Strain: 98/2 / Gene: Ssol_0413 / Production host: Escherichia coli (E. coli) / References: UniProt: D0KNS6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: evaporation
Details: magnesium sulfate heptahydrate, polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 24402 / % possible obs: 96.6 % / Redundancy: 5.7 % / Net I/σ(I): 21.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data processing
PHASERphasing
RefinementResolution: 2.501→42.589 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 1243 5.1 %
Rwork0.1962 --
obs0.1985 24370 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→42.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 3 203 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013835
X-RAY DIFFRACTIONf_angle_d1.1795181
X-RAY DIFFRACTIONf_dihedral_angle_d18.11477
X-RAY DIFFRACTIONf_chiral_restr0.05615
X-RAY DIFFRACTIONf_plane_restr0.006664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5013-2.60140.36721370.28362583X-RAY DIFFRACTION98
2.6014-2.71980.30781380.26642564X-RAY DIFFRACTION98
2.7198-2.86310.34531630.26162558X-RAY DIFFRACTION98
2.8631-3.04250.34191250.23782570X-RAY DIFFRACTION98
3.0425-3.27730.22361410.22092579X-RAY DIFFRACTION97
3.2773-3.60690.21481480.1942567X-RAY DIFFRACTION97
3.6069-4.12850.23911350.17392573X-RAY DIFFRACTION96
4.1285-5.20.20281330.16162550X-RAY DIFFRACTION95
5.2-42.59560.22741230.19452583X-RAY DIFFRACTION92

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