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- PDB-2n93: Solution structure of lcFABP -

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Basic information

Entry
Database: PDB / ID: 2n93
TitleSolution structure of lcFABP
ComponentsFatty acid-binding protein
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein
Similarity search - Component
Biological speciesLuciola cerata (firefly)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsTseng, K. / Lyu, P.
CitationJournal: Biomol NMR Assign / Year: 2016
Title: 1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies.
Authors: Tseng, K.L. / Lee, Y.Z. / Chen, Y.R. / Lyu, P.C.
History
DepositionNov 5, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein


Theoretical massNumber of molelcules
Total (without water)14,4511
Polymers14,4511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fatty acid-binding protein / lcFABP


Mass: 14450.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Luciola cerata (firefly) / Gene: FABP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G1FKW0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HN(CA)CO
1713D HNCO
1813D CC(CO)NH
1913D H(CCO)NH
11013D HBHA(CO)NH
11112D 1H-13C HSQC
11213D (H)CCH-TOCSY
11313D (H)CCH-COSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 0.9 mM [U-98% 13C; U-98% 15N] lcFABP-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 0.02 % sodium azide-4, 50 mM L-Arg-5, 10 % [U-100% 2H] D2O-6, 90 % H2O-7, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMlcFABP-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
0.02 %sodium azide-41
50 mML-Arg-51
10 %D2O-6[U-100% 2H]1
90 %H2O-71
Sample conditionsIonic strength: 0.3 / pH: 5.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ3.2Variancollection
VnmrJ3.2Varianprocessing
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2073 / NOE intraresidue total count: 517 / NOE long range total count: 675 / NOE medium range total count: 289 / NOE sequential total count: 592 / Protein phi angle constraints total count: 116 / Protein psi angle constraints total count: 116
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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