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- PDB-1bq0: J-DOMAIN (RESIDUES 1-77) OF THE ESCHERICHIA COLI N-TERMINAL FRAGM... -

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Basic information

Entry
Database: PDB / ID: 1bq0
TitleJ-DOMAIN (RESIDUES 1-77) OF THE ESCHERICHIA COLI N-TERMINAL FRAGMENT (RESIDUES 1-104) OF THE MOLECULAR CHAPERONE DNAJ, NMR, 20 STRUCTURES
ComponentsDNAJ
KeywordsCHAPERONE / HEAT SHOCK / PROTEIN FOLDING / DNAK
Function / homology
Function and homology information


sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein-disulfide reductase activity / protein unfolding / heat shock protein binding / viral process / unfolded protein binding / protein folding / protein-folding chaperone binding ...sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein-disulfide reductase activity / protein unfolding / heat shock protein binding / viral process / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / DNA replication / protein homodimerization activity / protein-containing complex / zinc ion binding / ATP binding / membrane / cytoplasm / cytosol
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 / DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. ...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 / DnaJ domain / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein DnaJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DG, SIMULATED ANNEALING
AuthorsHuang, K. / Flanagan, J.M. / Prestegard, J.H.
Citation
Journal: Protein Sci. / Year: 1999
Title: The influence of C-terminal extension on the structure of the "J-domain" in E. coli DnaJ.
Authors: Huang, K. / Flanagan, J.M. / Prestegard, J.H.
#1: Journal: Biochemistry / Year: 1995
Title: 1H and 15N Magnetic Resonance Assignments, Secondary Structure, and Tertiary Fold of Escherichia Coli Dnaj(1-78)
Authors: Hill, R.B. / Flanagan, J.M. / Prestegard, J.H.
History
DepositionAug 20, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNAJ


Theoretical massNumber of molelcules
Total (without water)11,4181
Polymers11,4181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50ZERO VIOLATIONS/ENERGY (SEE PAPER *JRNL*)
Representative

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Components

#1: Protein DNAJ / HSP40


Mass: 11417.551 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT (RESIDUES 1-104)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): MGT7 / References: UniProt: P08622

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE PAPER *JRNL*
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N LABELED PROTEIN

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Sample preparation

DetailsContents: 2MM, 10% D2O IN H2O
Sample conditionsIonic strength: 50 mM PHOSPHATE / pH: 6.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
GE OMEGAGEOMEGA5002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
XPLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DG, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS ARE IN THE PRIMARY JOURNAL REFERENCE
NMR ensembleConformer selection criteria: ZERO VIOLATIONS/ENERGY (SEE PAPER *JRNL*)
Conformers calculated total number: 50 / Conformers submitted total number: 20

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