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- PDB-1jy6: B4DIMERA: A DE NOVO DESIGNED FOUR-STRANDED BETA-SHEET ASSEMBLED U... -

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Basic information

Entry
Database: PDB / ID: 1jy6
TitleB4DIMERA: A DE NOVO DESIGNED FOUR-STRANDED BETA-SHEET ASSEMBLED USING A DISULFIDE BOND
ComponentsB4DIMER
KeywordsDE NOVO PROTEIN / four-stranded beta-sheet / disulfide bond / de novo protein design
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsVenkatraman, J. / Nagana Gowda, G.A. / Balaram, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Design and construction of an open multistranded beta-sheet polypeptide stabilized by a disulfide bridge.
Authors: Venkatraman, J. / Nagana Gowda, G.A. / Balaram, P.
History
DepositionSep 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B4DIMER
B: B4DIMER


Theoretical massNumber of molelcules
Total (without water)7,8752
Polymers7,8752
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)19 / 400structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #2closest to the average

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Components

#1: Protein/peptide B4DIMER


Mass: 3937.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide is chemically synthesized.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1mM B4dimer, trimethylsilylpropionate, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: unbuffered / pH: 3.5 / Pressure: ambient / Temperature: 323 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The nineteen structures were determined by NMR and torsion angle dynamics/simulated annealing methods. The peptide dimer was treated as a single entity and symmetry elements were not ...Details: The nineteen structures were determined by NMR and torsion angle dynamics/simulated annealing methods. The peptide dimer was treated as a single entity and symmetry elements were not utilized during structure calculations. The structures are based on a total of 276 NOE-derived restraints. The list of constraints is available in the file water_uppercons.txt. Structure calculations were performed with the program DYANA-1.5 (P. Guentert, C. Mumenthaler, K. Wuthrich, J. Mol. Biol.(1997)Vol.273, 283-298). No violation of distance constraints from NOEs exceeded 0.3Angstroms. The ensemble of structures is superimposed over the best-structured region encompasing residues V19-L34. Residues 1-11 were unstructured and their co-ordinates are not given. The average RMSDs between the superposed structures and the average structure are as follows: 1.04(chain A, residues 20-34, backbone atoms) 0.91(chain B, residues 20-34, backbone atoms).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 19

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