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- PDB-4ydz: Stress-induced protein 1 from Caenorhabditis elegans -

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Basic information

Entry
Database: PDB / ID: 4ydz
TitleStress-induced protein 1 from Caenorhabditis elegans
ComponentsStress-induced protein 1
KeywordsCHAPERONE / Molecular Chaperone / sHSP / Heat Shock / Protein Aggregation
Function / homology
Function and homology information


VEGFA-VEGFR2 Pathway / protein metabolic process / embryo development ending in birth or egg hatching / determination of adult lifespan / unfolded protein binding / response to heat / protein refolding / nucleus / cytosol / cytoplasm
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: 3.6 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 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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
C: Stress-induced protein 1
D: Stress-induced protein 1


Theoretical massNumber of molelcules
Total (without water)71,4654
Polymers71,4654
Non-polymers00
Water00
1
A: Stress-induced protein 1
B: Stress-induced protein 1
C: Stress-induced protein 1
D: Stress-induced protein 1
x 8


Theoretical massNumber of molelcules
Total (without water)571,71932
Polymers571,71932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation7_465y-1,x+1,-z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area94230 Å2
ΔGint-330.8 kcal/mol
Surface area183480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.550, 142.550, 100.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 200
2112C1 - 200
3122B1 - 200
4122D1 - 200

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.722259, -0.691572, -0.008403), (0.691535, 0.722308, -0.00713), (0.011, -0.000662, 0.999939)30.61249, 69.66161, 1.11085
3given(1), (1), (1)
4given(0.711725, -0.702459, -0.000419), (0.702429, 0.7117, -0.008813), (0.006489, 0.005977, 0.999961)29.69389, 71.08547, 0.35822

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Components

#1: Protein
Stress-induced protein 1 / Sip1


Mass: 17866.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sip-1, F43D9.4 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q20363

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES, 30% PEG 400, 100 mM NaAc

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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: Sep 3, 2011
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: 3.6→50 Å / Num. all: 12051 / Num. obs: 12051 / % possible obs: 96 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.6
Reflection shellResolution: 3.6→3.7 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 4.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3.6→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.907 / SU B: 26.886 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23909 603 5 %RANDOM
Rwork0.22019 ---
obs0.22116 11448 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.501 Å2
Baniso -1Baniso -2Baniso -3
1-4.95 Å20 Å20 Å2
2--4.95 Å2-0 Å2
3----9.9 Å2
Refinement stepCycle: 1 / Resolution: 3.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 0 0 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8441.9315074
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3235460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84125176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6115664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1831514
X-RAY DIFFRACTIONr_chiral_restr0.0590.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212802
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.53610.5771852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.27115.8462308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.43911.0221896
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.04385.7074908
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A531medium positional0.010.5
22B375medium positional0.010.5
11A540tight thermal11.170.5
22B388tight thermal6.260.5
11A531medium thermal11.052
22B375medium thermal6.492
LS refinement shellResolution: 3.6→3.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 42 -
Rwork0.31 807 -
obs--98.84 %

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