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- PDB-4yl9: Crystal Structure of wild-type of hsp14.1 from Sulfolobus solfata... -

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Basic information

Entry
Database: PDB / ID: 4yl9
TitleCrystal Structure of wild-type 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 / MOLECULAR REPLACEMENT / Resolution: 2.353 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)57,00511
Polymers56,6584
Non-polymers3477
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-54 kcal/mol
Surface area29550 Å2
Unit cell
Length a, b, c (Å)65.733, 39.108, 119.674
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14164.503 Da / Num. of mol.: 4
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 293 K / Method: evaporation
Details: calcium chloride dehydrate, 2-methyl-2,4-pentanediol, bis-tris (pH 6.5), ethylenediaminetetraacetic acid disodium salt dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 25552 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 13.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AAB

3aab


Resolution: 2.353→39.875 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 1314 5.16 %
Rwork0.2325 --
obs0.2335 25448 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.353→39.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 16 218 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093879
X-RAY DIFFRACTIONf_angle_d0.9315235
X-RAY DIFFRACTIONf_dihedral_angle_d22.5691492
X-RAY DIFFRACTIONf_chiral_restr0.068626
X-RAY DIFFRACTIONf_plane_restr0.011665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3527-2.44690.45071340.36792512X-RAY DIFFRACTION92
2.4469-2.55820.36961530.35052634X-RAY DIFFRACTION99
2.5582-2.6930.3371360.30782675X-RAY DIFFRACTION100
2.693-2.86170.30181390.28752701X-RAY DIFFRACTION99
2.8617-3.08260.3161580.26472653X-RAY DIFFRACTION99
3.0826-3.39270.25961500.23022683X-RAY DIFFRACTION99
3.3927-3.88330.18411440.19852739X-RAY DIFFRACTION100
3.8833-4.89110.18591510.18012735X-RAY DIFFRACTION99
4.8911-39.88070.24711490.22252802X-RAY DIFFRACTION98

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