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- PDB-5jtp: The structure of chaperone SecB in complex with unstructured proP... -

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Basic information

Entry
Database: PDB / ID: 5jtp
TitleThe structure of chaperone SecB in complex with unstructured proPhoA binding site e
Components
  • Alkaline phosphatase
  • Protein-export protein SecB
KeywordsCHAPERONE/HYDROLASE / Molecular Chaperone / CHAPERONE-HYDROLASE complex
Function / homology
Function and homology information


preprotein binding / maintenance of unfolded protein / oxidoreductase activity, acting on phosphorus or arsenic in donors / protein transport by the Sec complex / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / protein targeting / localization ...preprotein binding / maintenance of unfolded protein / oxidoreductase activity, acting on phosphorus or arsenic in donors / protein transport by the Sec complex / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / protein targeting / localization / dephosphorylation / protein dephosphorylation / protein tetramerization / protein localization / unfolded protein binding / protein transport / protein folding / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Bacterial protein export chaperone SecB / Preprotein translocase subunit SecB / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues ...Bacterial protein export chaperone SecB / Preprotein translocase subunit SecB / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline-phosphatase-like, core domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Alkaline phosphatase / Protein-export protein SecB / Protein-export protein SecB
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsHuang, C. / Saio, T. / Rossi, P. / Kalodimos, C.G.
CitationJournal: Nature / Year: 2016
Title: Structural basis for the antifolding activity of a molecular chaperone.
Authors: Huang, C. / Rossi, P. / Saio, T. / Kalodimos, C.G.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_database_status / pdbx_nmr_spectrometer
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-export protein SecB
B: Protein-export protein SecB
C: Protein-export protein SecB
D: Protein-export protein SecB
E: Alkaline phosphatase
F: Alkaline phosphatase
G: Alkaline phosphatase
H: Alkaline phosphatase


Theoretical massNumber of molelcules
Total (without water)78,7528
Polymers78,7528
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18780 Å2
ΔGint-102 kcal/mol
Surface area34240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein
Protein-export protein SecB


Mass: 17287.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: secB, Z5036, ECs4487 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AG88, UniProt: P0AG86*PLUS
#2: Protein/peptide
Alkaline phosphatase / / APase


Mass: 2400.789 Da / Num. of mol.: 4 / Fragment: residues 450-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: phoA, b0383, JW0374 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00634, alkaline phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic23D 1H-13C NOESY aliphatic
151isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] E.coli Chaperone SecB, 300 uM [U-100% 13C; U-100% 15N] E. Coli Alkaline Phosphatase (PhoA) binding site e, 150 mM potassium chloride, 50 mM sodium phosphate, ...Contents: 300 uM [U-100% 13C; U-100% 15N] E.coli Chaperone SecB, 300 uM [U-100% 13C; U-100% 15N] E. Coli Alkaline Phosphatase (PhoA) binding site e, 150 mM potassium chloride, 50 mM sodium phosphate, 50 mM potassium phosphate, 90% H2O/10% D2O
Details: 1H, 13C-ILVMAT Methyl labelling otherwise uniformly deuterated, 12C and 15N Specific labelling of aromatic residues
Label: Sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uME.coli Chaperone SecB[U-100% 13C; U-100% 15N]1
300 uME. Coli Alkaline Phosphatase (PhoA) binding site e[U-100% 13C; U-100% 15N]1
150 mMpotassium chloridenatural abundance1
50 mMsodium phosphatenatural abundance1
50 mMpotassium phosphatenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 301 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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