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- PDB-1r8t: Solution structures of high affinity miniprotein ligands to Strep... -

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Basic information

Entry
Database: PDB / ID: 1r8t
TitleSolution structures of high affinity miniprotein ligands to Streptavidin
ComponentsMP1
KeywordsUNKNOWN FUNCTION / miniprotein / streptavidin / high-affinity
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLuo, J. / Mukherjee, M. / Fan, X. / Yang, H. / Liu, D. / Khan, R. / White, M. / Fox, R.O.
CitationJournal: To be Published
Title: Structure-based design of high affinity miniprotein ligands
Authors: Luo, J. / Mukherjee, M. / Fan, X. / Yang, H. / Liu, D. / Khan, R. / White, M. / Fox, R.O.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Assembly

Deposited unit
A: MP1


Theoretical massNumber of molelcules
Total (without water)1,6871
Polymers1,6871
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)30 / 100structures with the lowest energy
RepresentativeModel #21lowest energy

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Components

#1: Protein/peptide MP1


Mass: 1687.003 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was identified to be a high affinity streptavidin binding ligand by phage display
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: This structure was determined using standard 2D homonuclear experiments.

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Sample preparation

DetailsContents: 1.3 mM MP1, 20mM sodium acetate(d3), pH 5.3, 90% H2O and 10% D2O
Solvent system: 90% H2O and 10% D2O
Sample conditionspH: 5.3 / Pressure: ambient / Temperature: 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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