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- PDB-1bpr: NMR STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF DNAK, MINIMIZED ... -

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Basic information

Entry
Database: PDB / ID: 1bpr
TitleNMR STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF DNAK, MINIMIZED AVERAGE STRUCTURE
ComponentsDNAKHsp70
KeywordsMOLECULAR CHAPERONE / HSP70 / PEPTIDE BINDING / PROTEIN FOLDING
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 / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
AuthorsWang, H. / Kurochkin, A.V. / Pang, Y. / Hu, W. / Flynn, G.C. / Zuiderweg, E.R.P.
CitationJournal: Biochemistry / Year: 1998
Title: NMR solution structure of the 21 kDa chaperone protein DnaK substrate binding domain: a preview of chaperone-protein interaction.
Authors: Wang, H. / Kurochkin, A.V. / Pang, Y. / Hu, W. / Flynn, G.C. / Zuiderweg, E.R.
History
DepositionAug 11, 1998Processing site: BNL
Revision 1.0Mar 2, 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNAK


Theoretical massNumber of molelcules
Total (without water)20,9401
Polymers20,9401
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)1 / 100TOTAL ENERGY
Representative

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Components

#1: Protein DNAK / Hsp70


Mass: 20940.344 Da / Num. of mol.: 1 / Fragment: SUBSTRATE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL-1 BLUE / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CA)HA
131HN(CO)CA
141HA(CACO)NH
151CP H(C)CCH-TOCSY
161CP (H)CCH-TOCSY
171CP (H)C(CCACO)NH-TOCSY
18115N-RESOLVED NOESY-HSQC
19113C RESOLVED NOESY-HMQC
11014D 13C RESOLVED HMQC-NOESY-HSQC
1111HNHA-J
NMR detailsText: THIS IS THE MEAN STRUCTURE

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: 50 mM INORGANIC PHOSPHATE / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

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Processing

NMR software
NameDeveloperClassification
DiscoverMSIrefinement
BIOSYMstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE REFERENCE CITED ABOVE
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 1

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