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- PDB-2n1e: MAX1 peptide fibril -

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Basic information

Entry
Database: PDB / ID: 2n1e
TitleMAX1 peptide fibril
ComponentsMAX1 peptide
KeywordsPROTEIN FIBRIL / designed peptide / hydrogel / biomaterials / amyloid-like / cross-beta
MethodSOLID-STATE NMR / molecular dynamics
AuthorsNagy-Smith, K. / Moore, E. / Schneider, J. / Tycko, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Molecular structure of monomorphic peptide fibrils within a kinetically trapped hydrogel network.
Authors: Nagy-Smith, K. / Moore, E. / Schneider, J. / Tycko, R.
History
DepositionMar 30, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 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 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAX1 peptide
B: MAX1 peptide
C: MAX1 peptide
D: MAX1 peptide
E: MAX1 peptide
F: MAX1 peptide
G: MAX1 peptide
H: MAX1 peptide


Theoretical massNumber of molelcules
Total (without water)17,8968
Polymers17,8968
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-94 kcal/mol
Surface area9660 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1last structure from namd trajectory

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Components

#1: Protein/peptide
MAX1 peptide


Mass: 2236.972 Da / Num. of mol.: 8 / Source method: obtained synthetically
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111REDOR
122REDOR
133REDOR
144REDOR
151PITHIRDS-CT
162PITHIRDS-CT
173PITHIRDS-CT
184PITHIRDS-CT
195PITHIRDS-CT
1106PITHIRDS-CT
1117PITHIRDS-CT
1128PITHIRDS-CT
113915N-BARE
114913C-BARE
115102D RAD/DARR
116102D NCACX
11792D RAD/DARR
11892D NCACX

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Sample preparation

Details
Solution-IDContentsSolvent system
113CO-V1, 15N-V20 MAX1, 100% H2O100% H2O
213CO-V3, 15N-V18 MAX1, 100% H2O100% H2O
313CO-V5, 15N-V16 MAX1, 100% H2O100% H2O
413CO-V7, 15N-V14 MAX1, 100% H2O100% H2O
513CO-V1, 13CO-V16 MAX1, 100% H2O100% H2O
613CO-V3, 13CO-V16 MAX1, 100% H2O100% H2O
713CO-V5, 13CO-V16 MAX1, 100% H2O100% H2O
813CO-V7, 13CO-V16 MAX1, 100% H2O100% H2O
913CO-P10; U-15N,13C-(K8, V9, )11, T12, K13) MAX1, 100% H2O100% H2O
10U-15N,13C-(V1, P11, T12, V20) MAX1, 100% H2O100% H2O
Sample
UnitsComponentIsotopic labelingSolution-ID
%MAX1-113CO-V1, 15N-V201
%MAX1-213CO-V3, 15N-V182
%MAX1-313CO-V5, 15N-V163
%MAX1-413CO-V7, 15N-V144
%MAX1-513CO-V1, 13CO-V165
%MAX1-613CO-V3, 13CO-V166
%MAX1-713CO-V5, 13CO-V167
%MAX1-813CO-V7, 13CO-V168
%MAX1-913CO-P10; U-15N,13C-(K8, V9, )11, T12, K13)9
%MAX1-10U-15N,13C-(V1, P11, T12, V20)10
Sample conditionsIonic strength: 0 / pH: 9 / Pressure: ambient / Temperature: 297 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InfinityPlusVarianInfinityplus4001
Bruker Avance IIIBrukerAVANCE III4002
Varian InfinityVarianInfinity7503

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NAMDSchulten, K. et al.structure solution
NAMDSchulten, K. et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: HYBRID MONTE CARLO/MOLECULAR DYNAMICS, USING NAMD TO GENERATE MC MOVES AND EXTERNAL PROGRAM TO ACCEPT OR REJECT MOVES BASED ON NMR-BASED POTENTIAL ENERGIES.
NMR representativeSelection criteria: last structure from namd trajectory
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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