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- PDB-5zul: Small heat shock protein from Mycobacterium marinum M : Form-3 -

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Basic information

Entry
Database: PDB / ID: 5zul
TitleSmall heat shock protein from Mycobacterium marinum M : Form-3
ComponentsSmall heat shock protein
KeywordsCHAPERONE / sHSP / oligomers / polydispersity
Function / homology: / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Molecular chaperone (Small heat shock protein)
Function and homology information
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 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
DepositionMay 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small heat shock protein
B: Small heat shock protein
C: Small heat shock protein
D: Small heat shock protein
E: Small heat shock protein
F: Small heat shock protein


Theoretical massNumber of molelcules
Total (without water)99,2156
Polymers99,2156
Non-polymers00
Water00
1
A: Small heat shock protein
B: Small heat shock protein
C: Small heat shock protein
D: Small heat shock protein
E: Small heat shock protein
F: Small heat shock protein

A: Small heat shock protein
B: Small heat shock protein
C: Small heat shock protein
D: Small heat shock protein
E: Small heat shock protein
F: Small heat shock protein


Theoretical massNumber of molelcules
Total (without water)198,43012
Polymers198,43012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area19730 Å2
ΔGint-100 kcal/mol
Surface area67960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.209, 128.420, 135.379
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


Mass: 16535.803 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: M / Gene: MMAR_2991 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / References: UniProt: B2HF11

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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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.05M MgCl2.6H2O, 0.1M HEPES pH 7.5 and 30% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.75→74.901 Å / Num. obs: 8296 / % possible obs: 97.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 114.3 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Net I/σ(I): 8.9
Reflection shellResolution: 3.75→4.19 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.724 / Num. unique obs: 2137 / CC1/2: 0.88 / Rpim(I) all: 0.254 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS3

5zs3


Resolution: 3.75→74.9 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.807 / SU B: 0.02 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.991 / ESU R Free: 1.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.40672 395 4.8 %RANDOM
Rwork0.36643 ---
obs0.36842 7883 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 166.701 Å2
Baniso -1Baniso -2Baniso -3
1--5.81 Å2-0 Å20 Å2
2---1.32 Å2-0 Å2
3---7.13 Å2
Refinement stepCycle: 1 / Resolution: 3.75→74.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 0 0 3878
LS refinement shellResolution: 3.75→3.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 25 -
Rwork0.404 583 -
obs--99.67 %

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