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- PDB-1exk: SOLUTION STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF THE ESCHERICHIA... -

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Basic information

Entry
Database: PDB / ID: 1exk
TitleSOLUTION STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF THE ESCHERICHIA COLI CHAPERONE PROTEIN DNAJ.
ComponentsDNAJ PROTEIN
KeywordsCHAPERONE / extended beta-hairpin / CXXCXGXG / zinc-binding motif
Function / homology
Function and homology information


sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein unfolding / protein-disulfide reductase activity / viral process / heat shock protein binding / unfolded protein binding / protein folding / protein-folding chaperone binding ...sigma factor antagonist activity / protein disulfide isomerase activity / chaperone cofactor-dependent protein refolding / protein unfolding / protein-disulfide reductase activity / viral process / heat shock protein binding / 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 / cytosol / cytoplasm
Similarity search - Function
Chaperone, DNAj Protein; Chain A / Heat shock protein DnaJ, cysteine-rich domain / 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 ...Chaperone, DNAj Protein; Chain A / Heat shock protein DnaJ, cysteine-rich domain / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chaperone protein DnaJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsMartinez-Yamout, M. / Legge, G.B. / Zhang, O. / Wright, P.E. / Dyson, H.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure of the cysteine-rich domain of the Escherichia coli chaperone protein DnaJ.
Authors: Martinez-Yamout, M. / Legge, G.B. / Zhang, O. / Wright, P.E. / Dyson, H.J.
History
DepositionMay 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNAJ PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6623
Polymers8,5311
Non-polymers1312
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 / 112structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #19closest to the average

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Components

#1: Protein DNAJ PROTEIN


Mass: 8530.705 Da / Num. of mol.: 1 / Fragment: RESIDUES 131-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: SYNTHETIC GENE BASED ON E. COLI DNAJ CRD SEQUENCE
Plasmid: PET24A / Production host: Escherichia coli (E. coli) / References: UniProt: P08622
#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: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 15N-separated NOESY
1213D 13C-separated NOESY
13113C/15N CN-NOESY
242HNHA
NMR detailsText: The sequence-specific assignments were completed using standard double and triple resonance NMR experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM DnaJ CRD U-15N,13C; 20 mM Tris-d11 pH 6.8; 300 uM ZnCl2; 50 mM NaCl; 2 mM DTT; 0.02% NaN395% H2O/5% D2O
2600 uM DnaJ CRD U-15N; 20 mM Tris-d11 pH 6.8; 300 uM ZnCl2; 50 mM NaCl;95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM 6.81 atm293 K
250 mM 6.81 atm293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
NMRView4.1.2Johnsondata analysis
SANE1Duggan and Leggedata analysis
DYANA1.5Guentertstructure solution
Amber6Caserefinement
SPIRIT1Zhuiterative matrix relaxation
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structures are based on 1361 unique NOE-based distance restraints and 99 torsion angle restaints and 24 stereo assignments.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 112 / Conformers submitted total number: 20

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