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- PDB-4ylc: Crystal Structure of Del-C4 mutant of hsp14.1 from Sulfolobus sol... -

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Basic information

Entry
Database: PDB / ID: 4ylc
TitleCrystal Structure of Del-C4 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


identical protein binding / metal ion 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: 3.1 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
E: Heat shock protein Hsp20
F: Heat shock protein Hsp20
G: Heat shock protein Hsp20
H: Heat shock protein Hsp20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,03317
Polymers111,7148
Non-polymers3199
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22670 Å2
ΔGint-207 kcal/mol
Surface area44020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.105, 189.105, 88.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 13964.202 Da / Num. of mol.: 8 / Fragment: C-terminal residues 121-124 deletion
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.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 12% w/v polyethylene glycol 3350, 0.1M sodium malonate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / 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: 3.1→50 Å / Num. obs: 28555 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 19.6
Reflection shellResolution: 3.1→3.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data processing
PHASERphasing
RefinementResolution: 3.1→44.572 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 1437 5.05 %
Rwork0.2397 --
obs0.2413 28435 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→44.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 9 93 6910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046896
X-RAY DIFFRACTIONf_angle_d0.8549350
X-RAY DIFFRACTIONf_dihedral_angle_d19.2522491
X-RAY DIFFRACTIONf_chiral_restr0.0361124
X-RAY DIFFRACTIONf_plane_restr0.0051206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.21090.33271300.32832650X-RAY DIFFRACTION98
3.2109-3.33940.35851440.29552682X-RAY DIFFRACTION100
3.3394-3.49130.33661410.27032685X-RAY DIFFRACTION100
3.4913-3.67530.31381380.26742696X-RAY DIFFRACTION100
3.6753-3.90540.31761270.24462718X-RAY DIFFRACTION100
3.9054-4.20680.28221700.22532668X-RAY DIFFRACTION100
4.2068-4.62970.23091650.20192699X-RAY DIFFRACTION100
4.6297-5.29870.23241260.21492719X-RAY DIFFRACTION100
5.2987-6.67220.28331440.2792729X-RAY DIFFRACTION100
6.6722-44.57710.24451520.22412752X-RAY DIFFRACTION99

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