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- PDB-5zs6: Dodecameric structure of a small Heat Shock Protein from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 5zs6
TitleDodecameric structure of a small Heat Shock Protein from Mycobacterium marinum M: Form-2
Components
  • GLY-ARG-LEU-LEU
  • Molecular chaperone (Small heat shock protein)
KeywordsCHAPERONE / sHSP / oligomers / polydispersity
Function / homology
Function and homology information


response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat
Similarity search - Function
: / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PROLINE / Molecular chaperone (Small heat shock protein)
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81191345712 Å
AuthorsBhandari, S. / Suguna, K.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Proteins / Year: 2019
Title: Dodecameric structure of a small heat shock protein from Mycobacterium marinum M.
Authors: Bhandari, S. / Biswas, S. / Chaudhary, A. / Dutta, S. / Suguna, K.
History
DepositionApr 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5229
Polymers16,9942
Non-polymers5277
Water362
1
A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules

A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,261108
Polymers203,93324
Non-polymers6,32984
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
MethodDODECAMERIC
Unit cell
Length a, b, c (Å)91.290, 91.290, 91.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AU

#1: Protein Molecular chaperone (Small heat shock protein)


Mass: 16535.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: M / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / References: UniProt: B2HF11
#2: Protein/peptide GLY-ARG-LEU-LEU


Mass: 458.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: M / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 9 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.92 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5 and 24 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.81→64.5516366332 Å / Num. obs: 3204 / % possible obs: 100 % / Redundancy: 21.9 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.045 / Net I/σ(I): 12.7
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 466 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GME

1gme


Resolution: 2.81191345712→64.55 Å / SU ML: 0.293615717533 / Cross valid method: FREE R-VALUE / σ(F): 1.35348710975 / Phase error: 17.2988004223
RfactorNum. reflection% reflection
Rfree0.250238558138 177 5.55555555556 %
Rwork0.199183007628 --
obs0.202519140461 3186 99.4692475804 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.38 Å2
Refinement stepCycle: LAST / Resolution: 2.81191345712→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 32 2 882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046298894019908
X-RAY DIFFRACTIONf_angle_d0.9226244599731226
X-RAY DIFFRACTIONf_chiral_restr0.054036055063146
X-RAY DIFFRACTIONf_plane_restr0.00619177403898158
X-RAY DIFFRACTIONf_dihedral_angle_d12.6331990058566
LS refinement shellResolution: 2.8119→2.9601 Å
RfactorNum. reflection% reflection
Rfree0.250238558138 177 -
Rwork0.199183007628 3009 -
obs--99.4692475804 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.138307119694.33268141887-5.982266638882.96618885681-3.371347951254.45307648066-0.3252545115011.29309221748-0.5607127374560.308508078124-0.4037324916720.2363324746790.3989371543730.1609994277580.5782155020820.5663494045110.2869618373060.06705348543860.75568814147-0.228774826650.70478325810322.956196747535.8167547866.8799934734
24.562306994080.444545214472-3.170604116513.330945746482.156365988453.98350246849-0.3032812703180.224618760959-0.475684330320.198640586705-0.1163639466640.01137729866830.695631208799-0.3405732953660.3788651376530.312854504879-0.06846469533150.04626314525610.3217867763910.01392798204170.32791161178816.975934397635.344782594953.0068036393
32.042357666630.530759425932-2.858981469911.5430345136-0.4469240791987.891388385610.114132692881-0.144538493782-0.3078570954410.017651062671-0.1312984128670.06678501853620.1211280065720.2319548404760.03392685483590.2077887387070.0178092881026-0.07666974220220.2237758537320.004784612984110.26153339473716.941620586136.979439442546.5662841051
40.9562811095850.168347692435-0.7651158346640.693899566477-0.2620461237580.9096545217270.0753227920113-0.736537201559-0.2085500041020.3724335507890.110360973675-0.0970802782931-0.140199194165-0.282090668766-0.199620968010.404632725531-0.119585163992-0.03283528424160.3385549961450.001626536223160.23370349792218.434539309736.148192813474.7717459895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'U' and (resid 1 through 4 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 109 )
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 130 )

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