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- PDB-2ksi: Solution NMR structure of Sterol Carrier Protein - 2 from Aedes a... -

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Basic information

Entry
Database: PDB / ID: 2ksi
TitleSolution NMR structure of Sterol Carrier Protein - 2 from Aedes aegypti (AeSCP-2) complex with C16 fatty acid (palmitate)
ComponentsSterol carrier protein 2
KeywordsLIPID BINDING PROTEIN / SCP-2 / Aedes Aegypti / palmitate
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
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsSingarapu, K. / Radek, J.T. / Tonelli, M. / Lan, Q. / Markley, J.L.
CitationJournal: To be Published
Title: Solution NMR structure of Sterol Carrier Protein - 2 from Aedes aegypti (AeSCP-2) complex with C16 fatty acid (palmitate)
Authors: Singarapu, K. / Radek, J.T. / Tonelli, M. / Markley, J.L. / Lan, Q.
History
DepositionJan 4, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Sterol carrier protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5442
Polymers12,2871
Non-polymers2561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Sterol carrier protein 2


Mass: 12287.228 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: SCP-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86PR3
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / 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
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HNCO
110115N,13C filtered 1H-13C NOESY
11122D 1H-15N HSQC
11222D 1H-15N TROSY
11332D 1H-15N HSQC
11432D 1H-15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-100% 13C; U-100% 15N] AeSCP-2-PA-1, 1 mM [U-100% 15N] AeSCP-2-PA-2, 93% H2O/7% D2O93% H2O/7% D2O
22 mM [U-100% 15N] AeSCP-2-PA-3, 93% H2O/7% D2O93% H2O/7% D2O
32 mM [U-100% 15N] AeSCP-2-PA-4, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMAeSCP-2-PA-1[U-100% 13C; U-100% 15N]1
1 mMAeSCP-2-PA-2[U-100% 15N]1
2 mMAeSCP-2-PA-3[U-100% 15N]2
2 mMAeSCP-2-PA-4[U-100% 15N]3
Sample conditionsIonic strength: 10 / pH: 7.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PSVSBhattacharya and Montelionedata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
VnmrJVariancollection
XEASYBartels et al.data analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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