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- PDB-2myj: Solution structure of a bacterial chaperone -

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Basic information

Entry
Database: PDB / ID: 2myj
TitleSolution structure of a bacterial chaperone
ComponentsAcid stress chaperone HdeB
KeywordsCHAPERONE
Function / homology
Function and homology information


cellular stress response to acidic pH / response to acidic pH / unfolded protein binding / outer membrane-bounded periplasmic space
Similarity search - Function
HNS-dependent expression B / 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 HdeB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsJin, C. / Hu, Y. / Ding, J.
CitationJournal: Sci Rep / Year: 2015
Title: HdeB chaperone activity is coupled to its intrinsic dynamic properties.
Authors: Ding, J. / Yang, C. / Niu, X. / Hu, Y. / Jin, C.
History
DepositionJan 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,1482
Polymers18,1482
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2355.1 Å2
ΔGint-20.4 kcal/mol
Surface area8667.7 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 HdeB / 10K-L protein


Mass: 9074.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: hdeB, yhhD, yhiC, b3509, JW5669 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AET2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCA
1713D HN(CO)CA
1813D HNCO
1913D (H)CCH-COSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D 1H-13C NOESY aromatic
11313D (H)CCH-TOCSY
11422D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-13C; U-15N] protein, 50 mM sodium phosphate, 45 mM citric acid, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-15N] protein, 50 mM sodium phosphate, 45 mM citric acid, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity_1-1[U-13C; U-15N]1
2 mMentity_2-2[U-13C; U-15N]1
50 mMsodium phosphate-31
45 mMcitric acid-41
1 mMentity_1-5[U-15N]2
1 mMentity_2-6[U-15N]2
50 mMsodium phosphate-72
45 mMcitric acid-82
Sample conditionsIonic strength: 0.17 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance7002
Bruker AvanceBrukerAvance8003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
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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