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- PDB-5v2g: De Novo Design of Novel Covalent Constrained Meso-size Peptide Sc... -

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Basic information

Entry
Database: PDB / ID: 5v2g
TitleDe Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures
Components20-mer Peptide
KeywordsDE NOVO PROTEIN / De Novo Design / Covalent Constrained peptide
Function / homology1,3,5-tris(bromomethyl)benzene
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsDang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D. / Baker, D. / DeGrado, W.F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures.
Authors: Dang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D.A. / Baker, D. / DeGrado, W.F.
History
DepositionMar 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 20-mer Peptide
B: 20-mer Peptide
C: 20-mer Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1594
Polymers6,8033
Non-polymers3571
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
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 20-mer Peptide


Mass: 2267.514 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ZBR / 1,3,5-tris(bromomethyl)benzene


Mass: 356.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9Br3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic1natural 13C -HSQC
141isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 0.7 mM non-label 1, 95% H2O/5% D2O / Details: 0.7mM, 50NaAC, pH 4.0, 5% D2O / Label: TP1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.7 mM / Component: 1 / Isotopic labeling: non-label
Sample conditionsDetails: 285K / Ionic strength: 50 mM / Ionic strength err: 1 / Label: con1 / pH: 4.0 / PH err: 0.1 / Pressure: 1 atm / Temperature: 285 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker advance II / Manufacturer: Bruker / Model: advance II / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxdata analysis
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: 20

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