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

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Basic information

Entry
Database: PDB / ID: 5jto
TitleThe structure of chaperone SecB in complex with unstructured proPhoA binding site d
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 / alkaline phosphatase / alkaline phosphatase activity / protein transport by the Sec complex / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / protein targeting / protein dephosphorylation ...preprotein binding / maintenance of unfolded protein / oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / protein transport by the Sec complex / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / protein targeting / protein dephosphorylation / protein tetramerization / unfolded protein binding / intracellular protein localization / protein folding / protein transport / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding / cytoplasm / cytosol
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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)86,4538
Polymers86,4538
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25600 Å2
ΔGint-162 kcal/mol
Surface area35600 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: 4325.987 Da / Num. of mol.: 4 / Fragment: residues 271-310
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
131isotropic22D 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 d, 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 d, 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 d[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
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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