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- PDB-1psv: COMPUTATIONALLY DESIGNED PEPTIDE WITH A BETA-BETA-ALPHA FOLD SELE... -

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Basic information

Entry
Database: PDB / ID: 1psv
TitleCOMPUTATIONALLY DESIGNED PEPTIDE WITH A BETA-BETA-ALPHA FOLD SELECTION, NMR, 32 STRUCTURES
ComponentsPDA8D
KeywordsDESIGNED PEPTIDE / PROTEIN DESIGN / DEAD END ELIMINATION / BETA-BETA-ALPHA FOLD / SEQUENCE OPTIMIZATION
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY-SIMULATED ANNEALING
AuthorsDahiyat, B.I. / Sarisky, C.A. / Mayo, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: De novo protein design: towards fully automated sequence selection.
Authors: Dahiyat, B.I. / Sarisky, C.A. / Mayo, S.L.
#1: Journal: Science / Year: 1997
Title: De Novo Protein Design: Fully Automated Sequence Selection
Authors: Dahiyat, B.I. / Mayo, S.L.
History
DepositionOct 29, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDA8D


Theoretical massNumber of molelcules
Total (without water)3,3691
Polymers3,3691
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)32 / 98NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS, RMS DEVIATIONS FROM IDEALIZED BOND LENGTHS < 0.01 A, AND RMS DEVIATIONS FROM IDEALIZED ANGLES AND IMPROPERS < 1.0 DEGREE
Representative

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Components

#1: Protein/peptide PDA8D


Mass: 3368.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE SELECTED BY DEAD END ELIMINATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY

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Sample preparation

Sample conditionspH: 5 / Temperature: 280 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
ANSIGstructure solution
X-PLORstructure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY-SIMULATED ANNEALING / Software ordinal: 1 / Details: SEE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS, RMS DEVIATIONS FROM IDEALIZED BOND LENGTHS < 0.01 A, AND RMS DEVIATIONS FROM IDEALIZED ANGLES AND IMPROPERS < 1.0 DEGREE
Conformers calculated total number: 98 / Conformers submitted total number: 32

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