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- PDB-3vqk: Small heat shock protein hsp14.0 of wild type -

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Basic information

Entry
Database: PDB / ID: 3vqk
TitleSmall heat shock protein hsp14.0 of wild type
ComponentsSmall heat shock protein StHsp14.0
KeywordsCHAPERONE / alpha-crystallin domain
Function / homologyHsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Small heat shock protein StHsp14.0
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsHanazono, Y. / Takeda, K. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural studies on the oligomeric transition of a small heat shock protein, StHsp14.0
Authors: Hanazono, Y. / Takeda, K. / Yohda, M. / Miki, K.
History
DepositionMar 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small heat shock protein StHsp14.0
B: Small heat shock protein StHsp14.0
C: Small heat shock protein StHsp14.0
D: Small heat shock protein StHsp14.0
E: Small heat shock protein StHsp14.0
F: Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)84,3856
Polymers84,3856
Non-polymers00
Water00
1
A: Small heat shock protein StHsp14.0
B: Small heat shock protein StHsp14.0
C: Small heat shock protein StHsp14.0
D: Small heat shock protein StHsp14.0
E: Small heat shock protein StHsp14.0
F: Small heat shock protein StHsp14.0

A: Small heat shock protein StHsp14.0
B: Small heat shock protein StHsp14.0
C: Small heat shock protein StHsp14.0
D: Small heat shock protein StHsp14.0
E: Small heat shock protein StHsp14.0
F: Small heat shock protein StHsp14.0

A: Small heat shock protein StHsp14.0
B: Small heat shock protein StHsp14.0
C: Small heat shock protein StHsp14.0
D: Small heat shock protein StHsp14.0
E: Small heat shock protein StHsp14.0
F: Small heat shock protein StHsp14.0

A: Small heat shock protein StHsp14.0
B: Small heat shock protein StHsp14.0
C: Small heat shock protein StHsp14.0
D: Small heat shock protein StHsp14.0
E: Small heat shock protein StHsp14.0
F: Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)337,54124
Polymers337,54124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area64420 Å2
ΔGint-271 kcal/mol
Surface area129350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.428, 117.428, 115.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Small heat shock protein StHsp14.0


Mass: 14064.229 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: hsp14.0, ST1653 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q970D9

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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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG2000MME, 4% glycerol, 4% sucrose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 16, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 4122 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.037 / Net I/σ(I): 42.6
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 350 / Rsym value: 0.45 / % possible all: 76.1

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AAB

3aab


Resolution: 4.5→37.13 Å / Rfactor Rfree error: 0.027 / Data cutoff high absF: 4571134.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.404 216 5.2 %RANDOM
Rwork0.333 ---
obs0.34 4119 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 189.635 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 278.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---1.56 Å20 Å2
3---3.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.08 Å1.09 Å
Luzzati d res low-5 Å
Luzzati sigma a-1.76 Å
Refinement stepCycle: LAST / Resolution: 4.5→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 0 0 5124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.5→4.78 Å / Rfactor Rfree error: 0.102 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.5 24 4.1 %
Rwork0.501 561 -
all-585 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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