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- PDB-6ber: Solution structure of de novo macrocycle design10.2 -

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Basic information

Entry
Database: PDB / ID: 6ber
TitleSolution structure of de novo macrocycle design10.2
ComponentsE(DVA)DP(DGL)(DHI)(DPR)N(DAL)(DPR)
KeywordsDE NOVO PROTEIN / macrocycle / de novo
Function / homologypolypeptide(D)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsShortridge, M.D. / Hosseinzadeh, P. / Pardo-Avila, F. / Varani, G. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)5R01GM103834 United States
CitationJournal: Science / Year: 2017
Title: Comprehensive computational design of ordered peptide macrocycles.
Authors: Hosseinzadeh, P. / Bhardwaj, G. / Mulligan, V.K. / Shortridge, M.D. / Craven, T.W. / Pardo-Avila, F. / Rettie, S.A. / Kim, D.E. / Silva, D.A. / Ibrahim, Y.M. / Webb, I.K. / Cort, J.R. / ...Authors: Hosseinzadeh, P. / Bhardwaj, G. / Mulligan, V.K. / Shortridge, M.D. / Craven, T.W. / Pardo-Avila, F. / Rettie, S.A. / Kim, D.E. / Silva, D.A. / Ibrahim, Y.M. / Webb, I.K. / Cort, J.R. / Adkins, J.N. / Varani, G. / Baker, D.
History
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 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.ptnr1_label_atom_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 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: E(DVA)DP(DGL)(DHI)(DPR)N(DAL)(DPR)


Theoretical massNumber of molelcules
Total (without water)1,1051
Polymers1,1051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1180 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Polypeptide(D) E(DVA)DP(DGL)(DHI)(DPR)N(DAL)(DPR)


Mass: 1105.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationY

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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 TOCSY
121isotropic12D 1H-1H NOESY
141isotropic22D 1H-1H NOESY
131isotropic22D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 5 mg/mL Design 10.2, 5 % v/v [U-2H] glycerol, 90% H2O/10% D2O
Label: Marie_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mg/mLDesign 10.2natural abundance1
5 % v/vglycerol[U-2H]1
Sample conditionsIonic strength: 0 Not defined / Label: cond_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
GROMACS2016.1Abrahamrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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