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- PDB-2lbv: Siderocalin Q83 reveals a dual ligand binding mode -

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Basic information

Entry
Database: PDB / ID: 2lbv
TitleSiderocalin Q83 reveals a dual ligand binding mode
ComponentsExtracellular fatty acid-binding protein
KeywordsLIPID TRANSPORT / Lipocalin / Siderocalin / Enterobactin / Arachidonic Acid
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
ARACHIDONIC ACID / Chem-EB4 / GALLIUM (III) ION / Extracellular fatty acid-binding protein
Similarity search - Component
Biological speciesCoturnix japonica (Japanese quail)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsCoudevylle, N. / Hoetzinger, M. / Geist, L. / Kontaxis, G. / Bister, K. / Konrat, R.
CitationJournal: Biochemistry / Year: 2011
Title: Lipocalin Q83 reveals a dual ligand binding mode with potential implications for the functions of siderocalins
Authors: Coudevylle, N. / Hoetzinger, M. / Geist, L. / Kontaxis, G. / Hartl, M. / Bister, K. / Konrat, R.
History
DepositionApr 7, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,1484
Polymers18,1051
Non-polymers1,0443
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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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


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


Mass: 69.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ga
#4: Chemical ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Siderocalin Q83 in complex with enterobactin and arachidonic acid
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CA)CB
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D HNHA
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic
11212D 1H-15N HSQC

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] Q83-1, 1mM Enterobactin-2, 1mM Gallium(III)-3, 1mM ARACHIDONIC ACID-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMQ83-1[U-100% 13C; U-100% 15N]1
1 mMEnterobactin-21
1 mMGallium(III)-31
1 mMARACHIDONIC ACID-41
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPiperefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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