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- PDB-4jus: Crystal structure of a fragment of Human HSPB6 -

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Basic information

Entry
Database: PDB / ID: 4jus
TitleCrystal structure of a 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 / negative regulation of cardiac muscle cell apoptotic process / : / protein folding chaperone / positive regulation of angiogenesis / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / nuclear speck ...structural constituent of eye lens / negative regulation of cardiac muscle cell apoptotic process / : / 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 kinase binding / 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: 2.5 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 / 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_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

Downloads & links

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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)88,44310
Polymers88,2598
Non-polymers1842
Water1,49583
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)44,2225
Polymers44,1304
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-19 kcal/mol
Surface area19780 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)44,2225
Polymers44,1304
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-29 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.592, 31.176, 152.149
Angle α, β, γ (deg.)90.000, 116.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-208-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 74:146 ) and (not resseq 100)...
21chain E and (resseq 74:146 ) and (not element H) and (not element D)
12chain C and (resseq 74:123 or resseq 133:146 ) and (not element H) and (not element D)
22chain G and (resseq 74:123 or resseq 133:146 ) and (not element H) and (not element D)
13chain D and (resseq 73:125 or resseq 127:146 ) and (not element H) and (not element D)
23chain H and (resseq 73:125 or resseq 127:146 ) and (not element H) and (not element D)
14chain B and (resseq 73:123 or resseq 132:147 ) and (not element H) and (not element D)
24chain F and (resseq 73:123 or resseq 132:147 ) and (not element H) and (not element D)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 74:146 ) and (not resseq 100)...A0
211chain 'E' and (resseq 74:146 ) and (not element H) and (not element D)E0
112chain 'C' and (resseq 74:123 or resseq 133:146 ) and (not element H) and (not element D)C74 - 123
122chain 'C' and (resseq 74:123 or resseq 133:146 ) and (not element H) and (not element D)C133 - 146
212chain 'G' and (resseq 74:123 or resseq 133:146 ) and (not element H) and (not element D)G74 - 123
222chain 'G' and (resseq 74:123 or resseq 133:146 ) and (not element H) and (not element D)G133 - 146
113chain 'D' and (resseq 73:125 or resseq 127:146 ) and (not element H) and (not element D)D73 - 125
123chain 'D' and (resseq 73:125 or resseq 127:146 ) and (not element H) and (not element D)D127 - 146
213chain 'H' and (resseq 73:125 or resseq 127:146 ) and (not element H) and (not element D)H73 - 125
223chain 'H' and (resseq 73:125 or resseq 127:146 ) and (not element H) and (not element D)H127 - 146
114chain 'B' and (resseq 73:123 or resseq 132:147 ) and (not element H) and (not element D)B73 - 123
124chain 'B' and (resseq 73:123 or resseq 132:147 ) and (not element H) and (not element D)B132 - 147
214chain 'F' and (resseq 73:123 or resseq 132:147 ) and (not element H) and (not element D)F73 - 123
224chain 'F' and (resseq 73:123 or resseq 132:147 ) and (not element H) and (not element D)F132 - 147

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 11032.407 Da / Num. of mol.: 8 / Fragment: UNP residues 57-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB6 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O14558
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.22 Å3/Da / Density % sol: 44.48 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M ammonium citrate, 21% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011
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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→30.633 Å / Num. all: 27616 / Num. obs: 27616 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.09 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.643.40.6590.5561.41366339930.350.6590.5562.399.8
2.64-2.83.50.4350.3682.11326937790.2290.4350.3683.699.8
2.8-2.993.60.3140.2662.91260135220.1650.3140.266599.7
2.99-3.233.60.220.1874.11196633230.1150.220.1876.999.9
3.23-3.543.60.1180.17.71093230700.0620.1180.111.799.4
3.54-3.953.50.0850.07210.6979627810.0450.0850.07215.999.5
3.95-4.563.50.0560.04814.6855424520.030.0560.0482299.3
4.56-5.593.40.0540.04515.6709220790.0290.0540.04523.299.3
5.59-7.913.30.0560.04615.6563216820.030.0560.04620.799.2
7.91-30.6333.20.030.02519.730189350.0170.030.0253097.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.633 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 0 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 1383 5.01 %Random
Rwork0.2091 ---
all0.212 27607 --
obs0.212 27607 99.37 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.622 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 114.38 Å2 / Biso mean: 47.1241 Å2 / Biso min: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.4645 Å2-0 Å2-14.8615 Å2
2---12.9295 Å20 Å2
3---11.465 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5211 0 12 83 5306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085365
X-RAY DIFFRACTIONf_angle_d1.0777315
X-RAY DIFFRACTIONf_chiral_restr0.065824
X-RAY DIFFRACTIONf_plane_restr0.006974
X-RAY DIFFRACTIONf_dihedral_angle_d14.5551945
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A550X-RAY DIFFRACTIONPOSITIONAL0.043
12E550X-RAY DIFFRACTIONPOSITIONAL0.043
21C516X-RAY DIFFRACTIONPOSITIONAL0.037
22G516X-RAY DIFFRACTIONPOSITIONAL0.037
31D579X-RAY DIFFRACTIONPOSITIONAL0.041
32H579X-RAY DIFFRACTIONPOSITIONAL0.041
41B537X-RAY DIFFRACTIONPOSITIONAL0.05
42F537X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58930.31981390.280826242763100
2.5893-2.6930.40881330.27225282661100
2.693-2.81540.35131390.253926342773100
2.8154-2.96380.30271340.226825372671100
2.9638-3.14930.27311390.212826352774100
3.1493-3.39220.24061360.18612607274399
3.3922-3.7330.21441380.187926072745100
3.733-4.27190.27321400.19912629276999
4.2719-5.37740.25531390.20132651279099
5.3774-30.63560.32361460.25552772291898

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