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- PDB-2n6i: NMR structure for a 2-stranded parallel beta-sheet -

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Basic information

Entry
Database: PDB / ID: 2n6i
TitleNMR structure for a 2-stranded parallel beta-sheet
Componentsdesigned 2-stranded parallel beta-sheet
KeywordsDE NOVO PROTEIN
MethodSOLUTION NMR / simulated annealing
AuthorsKung, V.M. / Cornilescu, G. / Gellman, S.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Impact of Strand Number on Parallel beta-Sheet Stability.
Authors: Kung, V.M. / Cornilescu, G. / Gellman, S.H.
History
DepositionAug 20, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Nov 6, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed 2-stranded parallel beta-sheet


Theoretical massNumber of molelcules
Total (without water)1,7281
Polymers1,7281
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide designed 2-stranded parallel beta-sheet


Mass: 1728.090 Da / Num. of mol.: 1 / Source method: obtained synthetically
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H ROESY
NMR detailsText: The authors state that the structures of these peptides in solution are more dynamic than are typical of well-ordered globular proteins such that the ROE intensities represent averages over ...Text: The authors state that the structures of these peptides in solution are more dynamic than are typical of well-ordered globular proteins such that the ROE intensities represent averages over multiple conformers. However, the authors make the simplifying assumption of there being a single set of structures. One result of this assumption is that reported clash scores are poorer than those typical of standard PDB structures. Warnings about residues that 'are not properly linked' and 'missing atoms' occur where there are non-natural residues and reversals in the chain directions, and there are no real problems with these stretches.

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Sample preparation

DetailsContents: 2 mM peptide, 2.5 mM acetic acid, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMpeptide-11
2.5 mMacetic acid-21
Sample conditionspH: 3.8 / Pressure: ambient / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: 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: 10

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