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- PDB-2ksh: Solution NMR structure of apo Sterol Carrier Protein - 2 from Aed... -

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Basic information

Entry
Database: PDB / ID: 2ksh
TitleSolution NMR structure of apo Sterol Carrier Protein - 2 from Aedes aegypti (AeSCP-2)
ComponentsSterol carrier protein 2
KeywordsLIPID BINDING PROTEIN / SCP-2
Function / homologyLipid-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 / Sterol carrier protein 2
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsSingarapu, N. / Radek, J.T. / Tonelli, M. / Lan, Q. / Markley, J.L.
CitationJournal: To be Published
Title: Solution NMR structure of apo Sterol Carrier Protein - 2 from Aedes aegypti (AeSCP-2)
Authors: Singarapu, N. / Radek, J.T. / Tonelli, M. / Lan, Q. / Markley, J.L.
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 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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:
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Assembly

Deposited unit
A: Sterol carrier protein 2


Theoretical massNumber of molelcules
Total (without water)12,2871
Polymers12,2871
Non-polymers00
Water0
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 least restraint violations
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

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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 HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HNCO
11022D 1H-15N HSQC
11122D 1H-15N TROSY
11232D 1H-15N HSQC
11332D 1H-15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-100% 13C; U-100% 15N] AeSCP-2, 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-100% 15N] AeSCP-2, 93% H2O/7% D2O93% H2O/7% D2O
31 mM [U-100% 15N] AESCP-2, 93% H2O/7% D2O, 15 mg/ml Pf1 phage93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMAeSCP-2-1[U-100% 13C; U-100% 15N]1
1 mMAeSCP-2-2[U-100% 15N]2
1 mMAeSCP-2-3[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 INOVAVarianINOVA9001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3P.GUNTERT ET AL.structure 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
CYANA3P.GUNTERT ET AL.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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