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- PDB-1q5l: NMR structure of the substrate binding domain of DnaK bound to th... -

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Basic information

Entry
Database: PDB / ID: 1q5l
TitleNMR structure of the substrate binding domain of DnaK bound to the peptide NRLLLTG
Components
  • Chaperone protein dnaK
  • peptide NRLLLTG
KeywordsCHAPERONE / Hsp70 / heat shock protein
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein DnaK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsStevens, S.Y. / Cai, S. / Pellecchia, M. / Zuiderweg, E.R.
CitationJournal: Protein Sci. / Year: 2003
Title: The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG.
Authors: Stevens, S.Y. / Cai, S. / Pellecchia, M. / Zuiderweg, E.R.
History
DepositionAug 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE REFERENCE FOR THE PEPTIDE IS GRAGEROV, A., ZENG, L., ZHAO, W., BURKHOLDER, W., AND ...SEQUENCE THE REFERENCE FOR THE PEPTIDE IS GRAGEROV, A., ZENG, L., ZHAO, W., BURKHOLDER, W., AND GOTTESMAN, M.E., SPECIFICITY OF DNAK-PEPTIDE BINDING. J.MOL. BIOL. (1994) 235, 848-854.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein dnaK
B: peptide NRLLLTG


Theoretical massNumber of molelcules
Total (without water)15,2582
Polymers15,2582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Chaperone protein dnaK / / Heat shock protein 70 / Heat shock 70 kDa protein / HSP70


Mass: 14471.352 Da / Num. of mol.: 1 / Fragment: substrate binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DNAK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8
#2: Protein/peptide peptide NRLLLTG / ASN-ARG-LEU-LEU-LEU-THR-GLY peptide


Mass: 786.941 Da / Num. of mol.: 1 / Fragment: sequence database residues 864-870 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131H(C)CH TOCSY
141(H)CCH TOCSY
15115N FILTERED/EDITED NOESY
16113C FILTERED/EDITED NOESY

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Sample preparation

DetailsContents: 0.66 mM DnaK(393-507); 3.3 mM NRLLLTG; 10 mM sodium phosphate buffer, pH 7.4
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate / pH: 7.4 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR2.6variancollection
VNMR2.6varianprocessing
NMRPipeDelaglioprocessing
XEASY3.2Wuthrichdata analysis
ARIA/(CNS)1Nilgesstructure solution
ARIA/(CNS)1Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 15

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