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- PDB-3aac: Small heat shock protein hsp14.0 with the mutations of I120F and ... -

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Basic information

Entry
Database: PDB / ID: 3aac
TitleSmall heat shock protein hsp14.0 with the mutations of I120F and I122F in the form II crystal
ComponentsPutative uncharacterized protein ST1653
KeywordsCHAPERONE / alpha-crystallin 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
Small heat shock protein StHsp14.0
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.4 Å
AuthorsTakeda, K. / Hayashi, T. / Abe, T. / Hirano, Y. / Hanazono, Y. / Yohda, M. / Miki, K.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Dimer structure and conformational variability in the N-terminal region of an archaeal small heat shock protein, StHsp14.0
Authors: Takeda, K. / Hayashi, T. / Abe, T. / Hirano, Y. / Hanazono, Y. / Yohda, M. / Miki, K.
History
DepositionNov 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Dec 25, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein ST1653
B: Putative uncharacterized protein ST1653


Theoretical massNumber of molelcules
Total (without water)28,2652
Polymers28,2652
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-11 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.564, 69.564, 49.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Putative uncharacterized protein ST1653 / small heat shock protein hsp14.0


Mass: 14132.262 Da / Num. of mol.: 2 / Mutation: I120F, I122F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST1653 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q970D9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 40% ethylene glycol, 200mM zinc acetate, 100mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 21, 2007 / Details: mirrors
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: 8995 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 39.187 Å2 / Rsym value: 0.076 / Net I/σ(I): 16.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 828 / Rsym value: 0.311 / % possible all: 88.7

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→34.97 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.688 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.275 432 4.81 %RANDOM
Rwork0.245 8556 --
obs-8988 95 %-
Solvent computationBsol: 51.006 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 59.61 Å2 / Biso mean: 19.87 Å2 / Biso min: 3.97 Å2
Baniso -1Baniso -2Baniso -3
1-37.508 Å20 Å20 Å2
2--37.508 Å20 Å2
3---21.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 0 19 1927
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.4941
X-RAY DIFFRACTIONf_bond_d0.0031
X-RAY DIFFRACTIONf_chiral_restr0.041
X-RAY DIFFRACTIONf_dihedral_angle_d10.4421
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0741

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