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- PDB-2kt4: Lipocalin Q83 is a Siderocalin -

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Basic information

Entry
Database: PDB / ID: 2kt4
TitleLipocalin Q83 is a Siderocalin
ComponentsExtracellular fatty acid-binding protein
KeywordsTRANSPORT PROTEIN / Siderocalin / Lipocalin / Enterobactin / Disulfide bond / Secreted / Transport
Function / homology
Function and homology information


oleic acid binding / enterobactin binding / arachidonic acid binding / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-EB4 / GALLIUM (III) ION / Extracellular fatty acid-binding protein
Similarity search - Component
Biological speciesCoturnix japonica (Japanese quail)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsCoudevylle, N. / Geist, L. / Hartl, M. / Kontaxis, G. / Bister, K. / Konrat, R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The v-myc-induced Q83 lipocalin is a siderocalin.
Authors: Coudevylle, N. / Geist, L. / Hotzinger, M. / Hartl, M. / Kontaxis, G. / Bister, K. / Konrat, R.
History
DepositionJan 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Extracellular fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8443
Polymers18,1051
Non-polymers7392
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Extracellular fatty acid-binding protein / Ex-FABP / Lipocalin Q83


Mass: 18104.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix japonica (Japanese quail) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I9P7
#2: Chemical ChemComp-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin / Enterobactin


Mass: 669.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27N3O15
#3: Chemical ChemComp-GA / GALLIUM (III) ION / Gallium


Mass: 69.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ga

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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
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
1101IPAP

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Sample preparation

DetailsContents: 1 mM [U-95% 13C; U-95% 15N] Q83, 1 mM Enterobactin, 1 mM Gallium, 0.5 mM DTT, 20 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMQ83-1[U-95% 13C; U-95% 15N]1
1 mMEnterobactin-21
1 mMGallium-31
0.5 mMDTT-41
20 mMpotassium phosphate-51
50 mMsodium chloride-61
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameDeveloperClassification
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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