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- PDB-5wyo: Solution structure of E.coli HdeA -

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Basic information

Entry
Database: PDB / ID: 5wyo
TitleSolution structure of E.coli HdeA
ComponentsAcid stress chaperone HdeA
KeywordsCHAPERONE / periplasmic protein
Function / homology
Function and homology information


cellular stress response to acidic pH / outer membrane-bounded periplasmic space
Similarity search - Function
HNS-dependent expression A / HNS-dependent expression A superfamily / HNS-dependent expression A / HNS-dependent expression A/B / HNS-dependent expression A/B superfamily / HdeA/HdeB family / 10k-s Protein, Hypothetical Protein A; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acid stress chaperone HdeA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, C. / Hu, Y. / Jin, C.
CitationJournal: Biochemistry / Year: 2017
Title: Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress
Authors: Yu, X.C. / Yang, C. / Ding, J. / Niu, X. / Hu, Y. / Jin, C.
History
DepositionJan 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid stress chaperone HdeA
B: Acid stress chaperone HdeA


Theoretical massNumber of molelcules
Total (without water)19,5062
Polymers19,5062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3530 Å2
ΔGint-32 kcal/mol
Surface area9990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Acid stress chaperone HdeA


Mass: 9752.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 / Gene: hdeA, Z4922, ECs4390 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AET0

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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
121isotropic23D HNCO
131isotropic23D HNCA
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB
161isotropic23D HBHA(CO)NH
171isotropic23D (H)CCH-TOCSY
181isotropic23D (H)CCH-COSY
191isotropic23D 1H-15N NOESY
1101isotropic23D 1H-13C NOESY
1111isotropic33D 13C/15N-filtered 13C-edited NOESY

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Sample preparation

DetailsType: solution
Contents: 2.0 mM [U-99% 13C; U-99% 15N] HdeA, 20 mM sodium citrate, 20 mM sodium phosphate, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMHdeA[U-99% 13C; U-99% 15N]1
20 mMsodium citratenatural abundance1
20 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 180 mM / Label: sample_condition_1 / pH: 3.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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