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- PDB-6jzb: Structural characterization of DnaJ from Streptococcus pneumonia ... -

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Basic information

Entry
Database: PDB / ID: 6jzb
TitleStructural characterization of DnaJ from Streptococcus pneumonia presents a new tetramer of Hsp40 family
ComponentsChaperone protein DnaJ
KeywordsSTRUCTURAL PROTEIN / cochaperone activity / zinc finger / tetramer
Function / homology
Function and homology information


heat shock protein binding / unfolded protein binding / protein folding / response to heat / DNA replication / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site ...Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
Chaperone protein DnaJ
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.754 Å
AuthorsZhu, M. / Zhu, Z.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaU1632124 China
CitationJournal: Biochimie / Year: 2020
Title: Structural insights into the formation of oligomeric state by a type I Hsp40 chaperone.
Authors: Zhu, M. / Ou, D. / Khan, M.H. / Zhao, S. / Zhu, Z. / Niu, L.
History
DepositionApr 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Chaperone protein DnaJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5753
Polymers41,4441
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16810 Å2
Unit cell
Length a, b, c (Å)47.584, 104.242, 234.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Chaperone protein DnaJ / / Heat shock protein 40


Mass: 41443.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: dnaJ_1, dnaJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0MSU1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→34.83 Å / Num. obs: 15553 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 72.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.15
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 777 / CC1/2: 0.902 / Χ2: 1.382 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.754→34.83 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.56
RfactorNum. reflection% reflection
Rfree0.2825 765 4.92 %
Rwork0.2488 --
obs0.2506 15534 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.754→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 2 0 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021925
X-RAY DIFFRACTIONf_angle_d1.4492594
X-RAY DIFFRACTIONf_dihedral_angle_d15.1821142
X-RAY DIFFRACTIONf_chiral_restr0.07286
X-RAY DIFFRACTIONf_plane_restr0.01350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7541-2.96660.34541420.31292911X-RAY DIFFRACTION99
2.9666-3.2650.35961470.28872905X-RAY DIFFRACTION100
3.265-3.73690.29241500.26712938X-RAY DIFFRACTION100
3.7369-4.70630.26821520.23792979X-RAY DIFFRACTION100
4.7063-34.83230.2651740.23033036X-RAY DIFFRACTION98

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