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- PDB-6ewn: HspA from Thermosynechococcus vulcanus in the presence of 2M urea... -

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Basic information

Entry
Database: PDB / ID: 6ewn
TitleHspA from Thermosynechococcus vulcanus in the presence of 2M urea with initial stages of denaturation
ComponentsHspA
KeywordsCHAPERONE / small Heat Shock Protein / cyanobacteria / denaturation / urea
Function / homology
Function and homology information


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
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsAdir, N. / Ghosh, S. / Salama, F. / Dines, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
ISF1045/06, 1576/12 and 843/16 Israel
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea.
Authors: Ghosh, S. / Salama, F. / Dines, M. / Lahav, A. / Adir, N.
History
DepositionNov 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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: HspA
B: HspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,90046
Polymers22,2572
Non-polymers2,64244
Water1,76598
1
A: HspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,09017
Polymers11,1291
Non-polymers96116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,81029
Polymers11,1291
Non-polymers1,68228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.650, 88.650, 114.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein HspA


Mass: 11128.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vulcanus (bacteria)
Gene: hspA / Production host: Escherichia coli (E. coli) / References: UniProt: O82825
#2: Chemical...
ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: CH4N2O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.4 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10mg/ml protein, 30%PEG MME, Tris-HCl pH=8.0 / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.29→70.03 Å / Num. obs: 19883 / % possible obs: 100 % / Redundancy: 4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.051 / Rrim(I) all: 0.107 / Net I/σ(I): 18.2
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 15.9 / Num. unique obs: 2887 / CC1/2: 0.915 / Rpim(I) all: 0.124 / Rrim(I) all: 0.278 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
SCALAdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GME

1gme


Resolution: 2.29→70.03 Å / Cross valid method: FREE R-VALUE / σ(F): 4 / Details: twinning operators used -h,k,-l
RfactorNum. reflection% reflectionSelection details
Rfree0.3419 1003 5 %Random selection
Rwork0.2803 ---
obs-19047 100 %-
Displacement parametersBiso max: 52.55 Å2 / Biso mean: 16.1473 Å2 / Biso min: 0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.29→70.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 176 98 1834

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