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- PDB-5ds1: Core domain of the class II small heat-shock protein HSP 17.7 fro... -

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Basic information

Entry
Database: PDB / ID: 5ds1
TitleCore domain of the class II small heat-shock protein HSP 17.7 from Pisum sativum
Components17.1 kDa class II heat shock protein
KeywordsCHAPERONE / sHSP / core domain
Function / homology
Function and homology information


: / 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
17.1 kDa class II heat shock protein
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsHochberg, G.K.A. / Laganoswky, A. / Allison, T.A. / Shepherd, D.A. / Benesch, J.L.P.
CitationJournal: Science / Year: 2018
Title: Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions.
Authors: Hochberg, G.K.A. / Shepherd, D.A. / Marklund, E.G. / Santhanagoplan, I. / Degiacomi, M.T. / Laganowsky, A. / Allison, T.M. / Basha, E. / Marty, M.T. / Galpin, M.R. / Struwe, W.B. / Baldwin, ...Authors: Hochberg, G.K.A. / Shepherd, D.A. / Marklund, E.G. / Santhanagoplan, I. / Degiacomi, M.T. / Laganowsky, A. / Allison, T.M. / Basha, E. / Marty, M.T. / Galpin, M.R. / Struwe, W.B. / Baldwin, A.J. / Vierling, E. / Benesch, J.L.P.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17.1 kDa class II heat shock protein
B: 17.1 kDa class II heat shock protein
C: 17.1 kDa class II heat shock protein


Theoretical massNumber of molelcules
Total (without water)31,9423
Polymers31,9423
Non-polymers00
Water181
1
A: 17.1 kDa class II heat shock protein

A: 17.1 kDa class II heat shock protein


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2790 Å2
ΔGint-7 kcal/mol
Surface area10650 Å2
MethodPISA
2
B: 17.1 kDa class II heat shock protein
C: 17.1 kDa class II heat shock protein


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-6 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 82.690, 88.900
Angle α, β, γ (deg.)90.00, 92.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 17.1 kDa class II heat shock protein


Mass: 10647.243 Da / Num. of mol.: 3 / Fragment: Core domains, UNP residues 43-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: HSP17.7 / Details (production host): pet28
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P19242
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 % / Description: Large rods
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: c17.7 was crystallized in 200 mM CaCl2, 100 mM sodium cacodylate pH 6.5, 40 % (v/v) polyethylene glycol (PEG) 200 in hanging drop plates at room temperature.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.63→35.02 Å / Num. obs: 10426 / % possible obs: 98.5 % / Redundancy: 3.53 % / Net I/σ(I): 7.34
Reflection shellResolution: 2.63→2.724 Å / Redundancy: 2.81 % / Mean I/σ(I) obs: 1.95 / CC1/2: 0.883 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DS2

5ds2


Resolution: 2.63→14.979 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2968 1041 9.99 %Random selection
Rwork0.2306 ---
obs0.2374 10419 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→14.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 1 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012060
X-RAY DIFFRACTIONf_angle_d1.1342768
X-RAY DIFFRACTIONf_dihedral_angle_d17.7721290
X-RAY DIFFRACTIONf_chiral_restr0.067334
X-RAY DIFFRACTIONf_plane_restr0.007351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6301-2.76790.34221440.28091291X-RAY DIFFRACTION96
2.7679-2.94010.41031460.29851325X-RAY DIFFRACTION99
2.9401-3.16520.34371500.29451346X-RAY DIFFRACTION99
3.1652-3.48010.32881490.25121346X-RAY DIFFRACTION100
3.4801-3.97540.29771490.22941346X-RAY DIFFRACTION100
3.9754-4.97790.25841500.19021355X-RAY DIFFRACTION100
4.9779-14.97950.26911530.21611369X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.69940.4784-1.20782.21152.33517.0834-0.3926-0.0064-0.19680.11410.3320.0480.3018-0.5957-0.03270.35920.0680.03020.27470.04880.4251-31.923912.66387.1857
24.5125-0.6821-2.71651.77251.08963.99620.16560.28570.3022-0.706-0.0694-0.0619-0.1032-0.5968-0.18690.4710.2564-0.00980.52650.08340.44-45.245927.315215.5476
32.49442.0142-1.95042.7865-1.27316.59510.4951-0.31220.57640.1334-0.48280.2364-0.6449-0.60690.04990.47590.22560.10160.7264-0.00140.4564-53.478332.05534.131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:94)
2X-RAY DIFFRACTION2(chain B and resseq 2:94)
3X-RAY DIFFRACTION3(chain C and resseq 2:95)

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