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- PDB-2g6u: Solution structures of MP-2: a high affinity miniprotein ligand t... -

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Basic information

Entry
Database: PDB / ID: 2g6u
TitleSolution structures of MP-2: a high affinity miniprotein ligand to Streptavidin
ComponentsMiniprotein MP2
KeywordsDE NOVO PROTEIN / miniprotein / type-1 beta turn / high affinity peptide to streptavidin
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsFox, R.O. / Mukherjee, M.
CitationJournal: To be Published
Title: Structural studies of high affinity miniprotein ligands to Streptavidin
Authors: Luo, J. / Mukherjee, M. / Fan, X. / Yang, H.W. / Liu, D. / Khan, R. / White, M. / Fox, R.O.
History
DepositionFeb 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Remark 999SEQUENCE THERE IS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Miniprotein MP2


Theoretical massNumber of molelcules
Total (without water)1,7831
Polymers1,7831
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 #1lowest energy

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Components

#1: Protein/peptide Miniprotein MP2


Mass: 1783.150 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear experiments

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Sample preparation

DetailsContents: 1.2mM MP-2 / Solvent system: 20mM Sod acetate; 90% H2O, 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Alex Brunger / Classification: refinement
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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