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- PDB-4ye0: Stress-induced protein 1 truncation mutant (43 - 140) from Caenor... -

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Basic information

Entry
Database: PDB / ID: 4ye0
TitleStress-induced protein 1 truncation mutant (43 - 140) from Caenorhabditis elegans
ComponentsStress-induced protein 1
KeywordsCHAPERONE / Molecular Chaperon / sHSP / Heat Shock / Protein Aggregation
Function / homology
Function and homology information


HSF1-dependent transactivation / protein metabolic process / embryo development ending in birth or egg hatching / determination of adult lifespan / unfolded protein binding / response to heat / protein refolding / nucleus / cytoplasm / cytosol
Similarity search - Function
Alpha crystallin/Small heat shock protein, animal type / 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
Stress-induced protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsFleckenstein, T. / Kastenmueller, A. / Stein, M.L. / Peters, C. / Daake, M. / Krause, M. / Weinfurtner, D. / Haslbeck, M. / Weinkauf, S. / Groll, M. / Buchner, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Mol.Cell / Year: 2015
Title: The Chaperone Activity of the Developmental Small Heat Shock Protein Sip1 Is Regulated by pH-Dependent Conformational Changes.
Authors: Fleckenstein, T. / Kastenmuller, A. / Stein, M.L. / Peters, C. / Daake, M. / Krause, M. / Weinfurtner, D. / Haslbeck, M. / Weinkauf, S. / Groll, M. / Buchner, J.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_nonpoly_scheme / struct_ncs_dom_lim
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stress-induced protein 1
B: Stress-induced protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2514
Polymers26,0592
Non-polymers1922
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.390, 50.820, 130.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 55 - 135 / Label seq-ID: 15 - 95

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.377508, 0.925904, -0.013792), (0.926, -0.377411, 0.009165), (0.003281, -0.016232, -0.999863)6.09111, -9.32176, 30.91599

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Components

#1: Protein Stress-induced protein 1


Mass: 13029.684 Da / Num. of mol.: 2 / Fragment: residues 43-159 / Mutation: Truncation mutant 1 - 43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sip-1, F43D9.4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q20363
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 33 mM CAPS, 17 mM BisTRIS, 17 mM ammoniumsulfate, 10% pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2012
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 14754 / Num. obs: 14754 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
PHASERphasing
RefinementResolution: 2.1→14.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 15.584 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25948 734 5 %RANDOM
Rwork0.23007 ---
obs0.23171 13947 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20 Å2
2--0.31 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.1→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 10 37 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191614
X-RAY DIFFRACTIONr_bond_other_d0.0020.021566
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9492183
X-RAY DIFFRACTIONr_angle_other_deg0.67533616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48825.06873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61115290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.752156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.06333180
X-RAY DIFFRACTIONr_sphericity_free33.514520
X-RAY DIFFRACTIONr_sphericity_bonded7.67353170
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
478medium positional0.210.5
796loose positional0.635
478medium thermal7.262
796loose thermal6.9710
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 53 -
Rwork0.372 1009 -
obs--99.72 %
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)
10.2077-0.2709-0.03660.3731-0.07922.0126-0.06650.0087-0.03960.07180.00230.01540.1346-0.10730.06420.0284-0.01190.02640.0397-0.01340.11292.77432.3494-0.8123
20.086-0.0869-0.0710.1563-0.17341.10880.02570.0392-0.0019-0.045-0.0694-0.01150.0648-0.03930.04370.0196-0.0001-0.00050.08830.00570.09749.4094-7.041232.0452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-41 - 140
2X-RAY DIFFRACTION2B-41 - 140

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