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- PDB-5zs3: Small heat shock protein from M. marinum:Form-1 -

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Basic information

Entry
Database: PDB / ID: 5zs3
TitleSmall heat shock protein from M. marinum:Form-1
Components
  • GLY-ARG-LEU-LEU-PRO
  • 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
Molecular chaperone (Small heat shock protein)
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 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 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,6109
Polymers17,3262
Non-polymers2847
Water54030
1
A: Molecular chaperone (Small heat shock protein)
U: GLY-ARG-LEU-LEU-PRO
hetero molecules

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

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

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

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

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

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

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

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)211,318108
Polymers207,91224
Non-polymers3,40684
Water43224
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
Unit cell
Length a, b, c (Å)91.140, 91.140, 91.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21A-202-

SO4

31A-205-

CL

41A-325-

HOH

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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: 16770.281 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-PRO


Mass: 555.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: M / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 37 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.91 Å3/Da / Density % sol: 31.61 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 2.1 M DL-Malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→64.45 Å / Num. obs: 8114 / % possible obs: 93.4 % / Redundancy: 12.3 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.052 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 11 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 634 / CC1/2: 0.825 / Rpim(I) all: 0.531 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→64.446 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.2453 377 4.65 %
Rwork0.1961 --
obs0.1984 8114 93.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.5 Å2
Refinement stepCycle: LAST / Resolution: 2.001→64.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 11 30 921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01906
X-RAY DIFFRACTIONf_angle_d1.2261234
X-RAY DIFFRACTIONf_dihedral_angle_d10.315757
X-RAY DIFFRACTIONf_chiral_restr0.07147
X-RAY DIFFRACTIONf_plane_restr0.009162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0013-2.29090.28211040.22932410X-RAY DIFFRACTION88
2.2909-2.88630.27221370.23752645X-RAY DIFFRACTION97
2.8863-64.47910.22741360.17412682X-RAY DIFFRACTION95
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)
10.0035-0.06990.03621.0267-0.55280.3017-0.1313-0.22570.05440.17850.23560.2775-0.0611-0.01560.18280.26460.03250.02160.2871-0.0820.147646.210524.48156.8779
20.056-0.04240.02530.0742-0.08010.06020.1186-0.1641-0.3339-0-0.02960.01340.0149-0.28270.00050.1629-0.0230.01190.28850.02520.208829.34715.453548.7623
30.09910.0871-0.01270.0888-0.02650.02990.1915-0.1323-0.47570.2958-0.1631-0.08170.2271-0.19820.00120.3589-0.03960.02960.40140.07940.354240.364714.874859.2484
40.05250.08850.07510.30460.13820.1682-0.019-0.14380.0854-0.0025-0.01590.0098-0.01260.1069-0.00010.17960.02340.00780.2898-0.01150.177353.953220.494552.956
50.12290.05190.02540.0252-0.02130.51560.1191-0.0820.03930.35430.08770.43310.5158-0.21020.02460.319-0.00240.08240.52930.09640.48723.707413.073960.1305
60.38480.131-0.02230.11940.11360.1824-0.22540.1447-0.4830.00410.07190.38670.0445-0.061-0.01120.196-0.00960.04830.270.07540.41222.030316.704353.4311
70.1750.0287-0.00370.1108-0.22240.46620.0027-0.00570.0090.0112-0.0551-0.1007-0.08250.049-0.3104-0.03650.05210.23760.0039-0.1114-0.019325.281323.765755.3394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 130 )
7X-RAY DIFFRACTION7chain 'U' and (resid 1 through 5 )

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