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- PDB-3vqm: Small heat shock protein hsp14.0 of C-terminal deletion variant w... -

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Basic information

Entry
Database: PDB / ID: 3vqm
TitleSmall heat shock protein hsp14.0 of C-terminal deletion variant with C-terminal peptide
Components
  • C-terminal peptide from Small heat shock protein StHsp14.0
  • Small heat shock protein StHsp14.0
KeywordsCHAPERONE / alpha-crystallin domain
Function / homologyImmunoglobulin-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 / Small heat shock protein StHsp14.0
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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

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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
G: Small heat shock protein StHsp14.0
H: Small heat shock protein StHsp14.0
I: Small heat shock protein StHsp14.0
J: Small heat shock protein StHsp14.0
K: Small heat shock protein StHsp14.0
L: Small heat shock protein StHsp14.0
M: Small heat shock protein StHsp14.0
N: Small heat shock protein StHsp14.0
O: C-terminal peptide from Small heat shock protein StHsp14.0
P: C-terminal peptide from Small heat shock protein StHsp14.0
Q: C-terminal peptide from Small heat shock protein StHsp14.0
R: C-terminal peptide from Small heat shock protein StHsp14.0
S: C-terminal peptide from Small heat shock protein StHsp14.0
T: C-terminal peptide from Small heat shock protein StHsp14.0
U: C-terminal peptide from Small heat shock protein StHsp14.0
V: C-terminal peptide from Small heat shock protein StHsp14.0
W: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)190,70923
Polymers190,70923
Non-polymers00
Water2,306128
1
A: Small heat shock protein StHsp14.0
B: Small heat shock protein StHsp14.0
O: C-terminal peptide from Small heat shock protein StHsp14.0
P: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)27,6744
Polymers27,6744
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Small heat shock protein StHsp14.0
D: Small heat shock protein StHsp14.0
Q: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)27,0723
Polymers27,0723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Small heat shock protein StHsp14.0
F: Small heat shock protein StHsp14.0
R: C-terminal peptide from Small heat shock protein StHsp14.0
S: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)27,6744
Polymers27,6744
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Small heat shock protein StHsp14.0
H: Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)26,4712
Polymers26,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Small heat shock protein StHsp14.0
J: Small heat shock protein StHsp14.0
T: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)27,0723
Polymers27,0723
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Small heat shock protein StHsp14.0
L: Small heat shock protein StHsp14.0
U: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)27,0723
Polymers27,0723
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Small heat shock protein StHsp14.0
N: Small heat shock protein StHsp14.0
V: C-terminal peptide from Small heat shock protein StHsp14.0
W: C-terminal peptide from Small heat shock protein StHsp14.0


Theoretical massNumber of molelcules
Total (without water)27,6744
Polymers27,6744
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.300, 161.900, 162.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Small heat shock protein StHsp14.0


Mass: 13235.255 Da / Num. of mol.: 14 / Mutation: deletion of 8 C-terminal residues
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
#2: Protein/peptide
C-terminal peptide from Small heat shock protein StHsp14.0


Mass: 601.755 Da / Num. of mol.: 9 / Source method: obtained synthetically
Details: This sequence is synthesized by the Fmoc solid phase method
References: UniProt: Q970D9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A-N ARE DELETION OF EIGHT C-TERMINAL RESIDUES

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM ammonium sulfate, 2.0% PEG8000, 15% glycerol, pH 8.0, 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: RAYONIX MX-225 / Detector: CCD / Date: Apr 20, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 65216 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.117 / Net I/σ(I): 12
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3085 / Rsym value: 0.396 / % possible all: 92.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AAB

3aab


Resolution: 2.55→42.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6700858.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3284 5.1 %RANDOM
Rwork0.224 ---
obs0.224 64958 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3269 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---6.71 Å20 Å2
3---7.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.55→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11877 0 0 128 12005
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.471.5
X-RAY DIFFRACTIONc_mcangle_it7.542
X-RAY DIFFRACTIONc_scbond_it8.032
X-RAY DIFFRACTIONc_scangle_it10.12.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 527 5.2 %
Rwork0.31 9672 -
obs--92.2 %
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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