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- PDB-2nbn: Solution NMR structure of palmitated SCP2L2 from Aedes aegypti -

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Basic information

Entry
Database: PDB / ID: 2nbn
TitleSolution NMR structure of palmitated SCP2L2 from Aedes aegypti
ComponentsSterol carrier protein 2-like 2
KeywordsLIPID TRANSPORT / SCP2L2 / Palmitate / Aedes aegypti
Function / homology
Function and homology information


Lipid-binding protein POX18/UbiT/NSL-TP1 / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Sterol carrier protein 2-like 2
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model1
AuthorsSingarapu, K.K. / Ummanni, R.
CitationJournal: Biochemistry / Year: 2016
Title: Solution Nuclear Magnetic Resonance Studies of Sterol Carrier Protein 2 Like 2 (SCP2L2) Reveal the Insecticide Specific Structural Characteristics of SCP2 Proteins in Aedes aegypti Mosquitoes
Authors: Singarapu, K.K. / Ahuja, A. / Potula, P.R. / Ummanni, R.
History
DepositionMar 7, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 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: Sterol carrier protein 2-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4543
Polymers11,9411
Non-polymers5132
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 Sterol carrier protein 2-like 2


Mass: 11940.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0GY13
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HBHA(CO)NH
1623D (H)CCH-COSY
1723D 1H-15N NOESY
1823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 15N] entity_1-1, 93% H2O/7% D2O93% H2O/7% D2O
21.0 mM [U-100% 13C; U-100% 15N] entity_1-2, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity_1-1[U-100% 15N]1
1.0 mMentity_1-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
ProcheckNMRLaskowski and MacArthurgeometry optimization
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry 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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