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- PDB-1k7b: NMR Solution Structure of sTva47, the Viral-Binding Domain of Tva -

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Basic information

Entry
Database: PDB / ID: 1k7b
TitleNMR Solution Structure of sTva47, the Viral-Binding Domain of Tva
ComponentsSUBGROUP A ROUS SARCOMA VIRUS RECEPTOR PG800 AND PG950
KeywordsMEMBRANE PROTEIN / BETA HAIRPIN / 3-10 HELIX / CALCIUM BINDING
Function / homology
Function and homology information


Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Low-density lipoprotein receptor domain class A / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Subgroup A Rous sarcoma virus receptor pg950
Similarity search - Component
Biological speciesCoturnix coturnix (Common quail)
MethodSOLUTION NMR / simulated annealing with torsion angle dynamics (DYANA), molecular dynamics (AMBER)
AuthorsTonelli, M. / Peters, R.J. / James, T.L. / Agard, D.A.
CitationJournal: FEBS Lett. / Year: 2001
Title: The solution structure of the viral binding domain of Tva, the cellular receptor for subgroup A avian leukosis and sarcoma virus.
Authors: Tonelli, M. / Peters, R.J. / James, T.L. / Agard, D.A.
History
DepositionOct 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_software.name / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: SUBGROUP A ROUS SARCOMA VIRUS RECEPTOR PG800 AND PG950


Theoretical massNumber of molelcules
Total (without water)5,1181
Polymers5,1181
Non-polymers00
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 #1lowest energy

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Components

#1: Protein/peptide SUBGROUP A ROUS SARCOMA VIRUS RECEPTOR PG800 AND PG950 / LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN


Mass: 5118.464 Da / Num. of mol.: 1 / Fragment: SOLUBLE EXTRACELLULAR VIRAL-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix coturnix (Common quail) / Plasmid: MBP-fusion PMAL / Production host: Escherichia coli (E. coli) / References: UniProt: P98162

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

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Sample preparation

DetailsContents: ~2mM sTva47 15N,13C; 50mM d3-NaAcetate; 5mM Calcium Cloride;
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.065 / pH: 5.5 / Pressure: ambient / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipesgi6xDelaglioprocessing
Sparky3Goddarddata analysis
DYANA1.5Guntertrefinement
Amber6Kollmanrefinement
RefinementMethod: simulated annealing with torsion angle dynamics (DYANA), molecular dynamics (AMBER)
Software ordinal: 1
Details: 1016 NOE-derived restraints: 120 intra, 346 sequential, 268 medium and 282 long-range restraints. The first 5 residues (S5-G9) show only intra-residue and sequential NOE connectivites and ...Details: 1016 NOE-derived restraints: 120 intra, 346 sequential, 268 medium and 282 long-range restraints. The first 5 residues (S5-G9) show only intra-residue and sequential NOE connectivites and were not included in our structural calculations.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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