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- PDB-4c26: Solution NMR structure of the HicA toxin from Burkholderia pseudo... -

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Basic information

Entry
Database: PDB / ID: 4c26
TitleSolution NMR structure of the HicA toxin from Burkholderia pseudomallei
ComponentsHICA2-Hydroxyisocaproic acid
KeywordsTOXIN
Function / homology
Function and homology information


endonuclease activity / mRNA binding
Similarity search - Function
Hypothetical protein. / HicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / Metal Transport, Frataxin; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Addiction module toxin, HicA family
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodSOLUTION NMR / TORSION-ANGLE DYNAMICS SIMULATED ANNEALING
AuthorsButt, A. / Higman, V.A. / Williams, C. / Crump, M.P. / Hemsley, C. / Harmer, N. / Titball, R.W.
CitationJournal: Biochem.J. / Year: 2014
Title: The Hica Toxin from Burkholderia Pseudomallei Has a Role in Persister Cell Formation.
Authors: Butt, A. / Higman, V.A. / Williams, C. / Crump, M.P. / Hemsley, C.M. / Harmer, N. / Titball, R.W.
History
DepositionAug 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Atomic model / Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HICA


Theoretical massNumber of molelcules
Total (without water)7,3281
Polymers7,3281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein HICA / 2-Hydroxyisocaproic acid


Mass: 7327.580 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q63NA6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N NOESY
22115N TOCSY
331HNHA
441HSQC
55113C HSQC
66113C NOESY
771AROM NOESY
881(H)CCH TOCSY
991HNCA
10101HNCO
111112D NOESY
NMR detailsText: NONE

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Sample preparation

Details
Solution-IDContents
190% H2O/10% D2O
290% H2O/10% D2O
390% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1170 mM7.4 1.0 atm298.0 K
2170 mM7.4 1.0 atm298.0 K
3170 mM7.4 1.0 atm293.0 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3RIEPING W., HABECK M., BARDIAUX B., BERNARD A., MALLIAVIN T.E., NILGES M.refinement
ARIA2.3structure solution
CCNMRANALYSIS2.2structure solution
DANGLEstructure solution
RefinementMethod: TORSION-ANGLE DYNAMICS SIMULATED ANNEALING / Software ordinal: 1 / Details: WATER REFINEMENT
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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