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- PDB-4jut: Crystal structure of a mutant fragment of Human HSPB6 -

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Basic information

Entry
Database: PDB / ID: 4jut
TitleCrystal structure of a mutant fragment of Human HSPB6
ComponentsHeat shock protein beta-6
KeywordsCHAPERONE / Small heat shock protein / alpha-crystallin domain
Function / homology
Function and homology information


structural constituent of eye lens / chaperone-mediated protein folding / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck / negative regulation of apoptotic process ...structural constituent of eye lens / chaperone-mediated protein folding / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / 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
Heat shock protein beta-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.196 Å
AuthorsWeeks, S.D. / Baranova, E.V. / Beelen, S. / Heirbaut, M. / Gusev, N.B. / Strelkov, S.V.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Molecular structure and dynamics of the dimeric human small heat shock protein HSPB6.
Authors: Weeks, S.D. / Baranova, E.V. / Heirbaut, M. / Beelen, S. / Shkumatov, A.V. / Gusev, N.B. / Strelkov, S.V.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein beta-6
B: Heat shock protein beta-6
C: Heat shock protein beta-6
D: Heat shock protein beta-6
E: Heat shock protein beta-6
F: Heat shock protein beta-6
G: Heat shock protein beta-6
H: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49314
Polymers88,9408
Non-polymers5536
Water3,171176
1
A: Heat shock protein beta-6
B: Heat shock protein beta-6
C: Heat shock protein beta-6
D: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7467
Polymers44,4704
Non-polymers2763
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-29 kcal/mol
Surface area17830 Å2
MethodPISA
2
E: Heat shock protein beta-6
F: Heat shock protein beta-6
G: Heat shock protein beta-6
H: Heat shock protein beta-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7467
Polymers44,4704
Non-polymers2763
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-26 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.440, 86.010, 87.070
Angle α, β, γ (deg.)90.000, 108.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Heat shock protein beta-6 / HspB6 / Heat shock 20 kDa-like protein p20


Mass: 11117.516 Da / Num. of mol.: 8 / Fragment: UNP residues 57-160 / Mutation: E51A, E52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB6 / Plasmid: pPEPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14558
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M litium nitrate, 20% PEG 3350, hanging drop vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2008
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.196→43.01 Å / Num. all: 49462 / Num. obs: 49462 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 38.7 Å2 / Rsym value: 0.077

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.196→43.005 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 2499 5.05 %Random
Rwork0.1964 ---
all0.1991 49452 --
obs0.1991 49452 99.4 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.102 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 127.93 Å2 / Biso mean: 43.7462 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.1251 Å20 Å20.0079 Å2
2---0.89 Å20 Å2
3---0.7649 Å2
Refinement stepCycle: LAST / Resolution: 2.196→43.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 0 36 176 5467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095452
X-RAY DIFFRACTIONf_angle_d1.1647441
X-RAY DIFFRACTIONf_chiral_restr0.078828
X-RAY DIFFRACTIONf_plane_restr0.006994
X-RAY DIFFRACTIONf_dihedral_angle_d13.0271973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1965-2.23870.36761180.30772366248490
2.2387-2.28440.3471520.299725472699100
2.2844-2.33410.31941550.26426092764100
2.3341-2.38840.32871150.264426492764100
2.3884-2.44810.31291340.265926202754100
2.4481-2.51430.3251490.248826062755100
2.5143-2.58830.3221230.225126242747100
2.5883-2.67180.26971310.220826162747100
2.6718-2.76730.27851370.225226422779100
2.7673-2.87810.28771510.223125782729100
2.8781-3.0090.29051440.207826182762100
3.009-3.16760.28051540.220625982752100
3.1676-3.3660.26711370.196226262763100
3.366-3.62580.22321350.191726532788100
3.6258-3.99040.2511290.194526252754100
3.9904-4.56730.18481490.16526332782100
4.5673-5.75210.22231500.159526502800100
5.7521-43.01320.23951360.194126932829100

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