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- PDB-3w1z: Heat shock protein 16.0 from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 3w1z
TitleHeat shock protein 16.0 from Schizosaccharomyces pombe
ComponentsHeat shock protein 16Heat shock response
KeywordsCHAPERONE / alpha-crystallin domain / small heat shock protein
Function / homology
Function and homology information


protein aggregate center / cellular response to misfolded protein / cellular response to unfolded protein / chaperone-mediated protein folding / unfolded protein binding / cellular response to heat / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 16
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsHanazono, Y. / Takeda, K. / Akiyama, N. / Aikawa, Y. / Miki, K.
CitationJournal: Structure / Year: 2013
Title: Nonequivalence Observed for the 16-Meric Structure of a Small Heat Shock Protein, SpHsp16.0, from Schizosaccharomyces pombe
Authors: Hanazono, Y. / Takeda, K. / Oka, T. / Abe, T. / Tomonari, T. / Akiyama, N. / Aikawa, Y. / Yohda, M. / Miki, K.
History
DepositionNov 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16


Theoretical massNumber of molelcules
Total (without water)63,9524
Polymers63,9524
Non-polymers00
Water1,67593
1
A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16

A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16

A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16

A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16


Theoretical massNumber of molelcules
Total (without water)255,80616
Polymers255,80616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area63940 Å2
ΔGint-136 kcal/mol
Surface area93720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.296, 121.078, 122.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Heat shock protein 16 / Heat shock response / 16 kDa heat shock protein


Mass: 15987.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: hsp16 / Production host: Escherichia coli (E. coli) / References: UniProt: O14368
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 15% PEGMME550, 100mM sodium chloride, 100mM Bicine buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22653 / % possible obs: 97.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.13 Å2 / Rsym value: 0.043 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.254 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GME

1gme


Resolution: 2.401→44.834 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7417 / SU ML: 0.41 / σ(F): 0 / Phase error: 31.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1154 5.1 %random
Rwork0.2457 ---
obs0.2478 22645 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.45 Å2 / Biso mean: 51.4625 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: LAST / Resolution: 2.401→44.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 93 4159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054191
X-RAY DIFFRACTIONf_angle_d1.0495668
X-RAY DIFFRACTIONf_chiral_restr0.072643
X-RAY DIFFRACTIONf_plane_restr0.005749
X-RAY DIFFRACTIONf_dihedral_angle_d16.4661610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4006-2.50980.40221580.33332567272595
2.5098-2.64220.351490.30922585273496
2.6422-2.80770.31091440.29072617276197
2.8077-3.02440.31311260.27152665279197
3.0244-3.32870.31271480.25082678282699
3.3287-3.81010.28861410.234927462887100
3.8101-4.79950.26051500.21692749289999
4.7995-44.84160.23811380.22422884302299

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