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- PDB-6l6m: HSP18.5 from E. histolytica -

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Basic information

Entry
Database: PDB / ID: 6l6m
TitleHSP18.5 from E. histolytica
ComponentsHeat shock protein hsp20 family putative
KeywordsCHAPERONE / Small heat shock protein HSP18.5 Molecular chaperone E. histolytica
Function / homologyHsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Heat shock protein, Hsp20 family, putative
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28000381979 Å
AuthorsKurre, D. / Suguna, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/005407 India
CitationJournal: Proteins / Year: 2021
Title: Network of Entamoeba histolytica HSP18.5 dimers formed by two overlapping [IV]-X-[IV] motifs.
Authors: Kurre, D. / Suguna, K.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein hsp20 family putative
B: Heat shock protein hsp20 family putative
C: Heat shock protein hsp20 family putative
D: Heat shock protein hsp20 family putative


Theoretical massNumber of molelcules
Total (without water)75,3944
Polymers75,3944
Non-polymers00
Water00
1
A: Heat shock protein hsp20 family putative
C: Heat shock protein hsp20 family putative

B: Heat shock protein hsp20 family putative
D: Heat shock protein hsp20 family putative


Theoretical massNumber of molelcules
Total (without water)75,3944
Polymers75,3944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area7590 Å2
ΔGint-51 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.237, 173.988, 159.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Heat shock protein hsp20 family putative / Heat shock protein / Hsp20 family / putative


Mass: 18848.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_193390, EHI_193390 / Production host: Escherichia coli (E. coli) / References: UniProt: C4M4U3

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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: 3.32 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M Bis-Tris 160 mM ammonium acetate 45% 2-Methyl-2,4-pentanediol
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.991872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991872 Å / Relative weight: 1
ReflectionResolution: 3.28→79.53 Å / Num. obs: 15560 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 112.375814491 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.99
Reflection shellResolution: 3.28→3.43 Å / Num. unique obs: 2004 / CC1/2: 0.99 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1Z

3w1z


Resolution: 3.28000381979→79.529 Å / SU ML: 0.359075090824 / Cross valid method: FREE R-VALUE / σ(F): 1.91706635515 / Phase error: 24.653739223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.22750744055 769 4.94501961289 %random selection
Rwork0.187278420596 14782 --
obs0.189283205598 15551 99.90363613 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.2352389117 Å2
Refinement stepCycle: LAST / Resolution: 3.28000381979→79.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 0 0 3260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023249110023351
X-RAY DIFFRACTIONf_angle_d1.048806232784579
X-RAY DIFFRACTIONf_chiral_restr0.0577420152582512
X-RAY DIFFRACTIONf_plane_restr0.00629784085347589
X-RAY DIFFRACTIONf_dihedral_angle_d9.192457067472163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28000381979-3.53330.2700485039941890.2408425110422864X-RAY DIFFRACTION99.8038574698
3.5333-3.88880.2515415393671380.1970205059812929X-RAY DIFFRACTION100
3.8888-4.45150.2285024210151450.1642894918392944X-RAY DIFFRACTION99.9676375405
4.4515-5.60820.2001227623841570.1659872192982954X-RAY DIFFRACTION99.9678663239
5.6082-79.5290.229059145141400.1989336316613091X-RAY DIFFRACTION99.7838171711

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