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- PDB-7ck4: Structural and functional analysis of small heat shock protein fr... -

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Basic information

Entry
Database: PDB / ID: 7ck4
TitleStructural and functional analysis of small heat shock protein from Synechococcus phage S-ShM2
ComponentsHeat shock protein
KeywordsCHAPERONE / small heat shock protein / oligomers / nanocage / chaperone activity.
Function / homologyHsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Heat shock protein
Function and homology information
Biological speciesSynechococcus phage S-ShM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsBiswas, S. / Suguna, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST-1865 India
CitationJournal: Sci Rep / Year: 2021
Title: Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries.
Authors: Sreeparna Biswas / Priyanka Garg / Somnath Dutta / Kaza Suguna /
Abstract: The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa ...The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.
History
DepositionJul 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Aug 4, 2021Group: Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.3Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein
B: Heat shock protein
C: Heat shock protein
D: Heat shock protein
E: Heat shock protein
F: Heat shock protein


Theoretical massNumber of molelcules
Total (without water)116,9566
Polymers116,9566
Non-polymers00
Water00
1
A: Heat shock protein
B: Heat shock protein
C: Heat shock protein
D: Heat shock protein
E: Heat shock protein
F: Heat shock protein

A: Heat shock protein
B: Heat shock protein
C: Heat shock protein
D: Heat shock protein
E: Heat shock protein
F: Heat shock protein

A: Heat shock protein
B: Heat shock protein
C: Heat shock protein
D: Heat shock protein
E: Heat shock protein
F: Heat shock protein

A: Heat shock protein
B: Heat shock protein
C: Heat shock protein
D: Heat shock protein
E: Heat shock protein
F: Heat shock protein


Theoretical massNumber of molelcules
Total (without water)467,82524
Polymers467,82524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)126.146, 126.146, 152.900
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 / small heat shock protein


Mass: 19492.713 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus phage S-ShM2 (virus) / Gene: hsp20, SShM2_166 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3SJI7

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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: 2.42 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium sulphate monohydrate, 0.1M Tris, 25% PEG 3350
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9536 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 7→48.7 Å / Num. obs: 1915 / % possible obs: 99.4 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.164 / Net I/σ(I): 9.5
Reflection shellResolution: 7→7.83 Å / Rmerge(I) obs: 1.53 / Num. unique obs: 557 / CC1/2: 0.628 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJA

4zja


Resolution: 7→48.65 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.704 / SU ML: 21.101 / Cross valid method: THROUGHOUT / ESU R Free: 5.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.4335 99 5.2 %RANDOM
Rwork0.34566 ---
obs0.35063 1816 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 490.032 Å2
Baniso -1Baniso -2Baniso -3
1--4.88 Å20 Å20 Å2
2---4.88 Å20 Å2
3---9.76 Å2
Refinement stepCycle: 1 / Resolution: 7→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 0 0 4678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0155098
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174611
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.7396929
X-RAY DIFFRACTIONr_angle_other_deg0.3811.70210816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6325614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.31119.944177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1415744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0661524
X-RAY DIFFRACTIONr_chiral_restr0.0460.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it24.67850.732474
X-RAY DIFFRACTIONr_mcbond_other24.67350.7282475
X-RAY DIFFRACTIONr_mcangle_it42.84276.0783082
X-RAY DIFFRACTIONr_mcangle_other42.83676.0743083
X-RAY DIFFRACTIONr_scbond_it19.2250.7322624
X-RAY DIFFRACTIONr_scbond_other19.22150.7362623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other35.85676.1293848
X-RAY DIFFRACTIONr_long_range_B_refined68.5395168
X-RAY DIFFRACTIONr_long_range_B_other68.5335169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.001→7.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.154 6 -
Rwork0.21 136 -
obs--100 %

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