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- PDB-1abz: ALPHA-T-ALPHA, A DE NOVO DESIGNED PEPTIDE, NMR, 23 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1abz
TitleALPHA-T-ALPHA, A DE NOVO DESIGNED PEPTIDE, NMR, 23 STRUCTURES
ComponentsALPHA-T-ALPHA
KeywordsDE NOVO DESIGN / HELIX-TURN-HELIX
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY DYNAMICAL SIMULATED ANNEALING
AuthorsFezoui, Y. / Connolly, P.J. / Osterhout, J.J.
Citation
Journal: Protein Sci. / Year: 1997
Title: Solution structure of alpha t alpha, a helical hairpin peptide of de novo design.
Authors: Fezoui, Y. / Connolly, P.J. / Osterhout, J.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: De Novo Design and Structural Characterization of an Alpha-Helical Hairpin Peptide: A Model System for the Study of Protein Folding Intermediates
Authors: Fezoui, Y. / Weaver, D.L. / Osterhout, J.J.
History
DepositionJan 31, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-T-ALPHA


Theoretical massNumber of molelcules
Total (without water)4,4461
Polymers4,4461
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)23 / 100
Representative

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Components

#1: Protein/peptide ALPHA-T-ALPHA / ATA


Mass: 4446.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DE NOVO DESIGNED PEPTIDE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR TWO-DIMENSIONAL NMR SPECTROSCOPY.

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Sample preparation

Sample conditionspH: 3.6 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 400 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY DYNAMICAL SIMULATED ANNEALING
Software ordinal: 1
Details: THE FAMILY OF 23 STRUCTURES IS SUPERIMPOSED OVER THE WELL-DEFINED HELICAL REGION ENCOMPASSING RESIDUES 4 - 16 AND 24 - 34. THE AVERAGE RMSD'S BETWEEN THE 23 REFINED STRUCTURES AND AVERAGE ...Details: THE FAMILY OF 23 STRUCTURES IS SUPERIMPOSED OVER THE WELL-DEFINED HELICAL REGION ENCOMPASSING RESIDUES 4 - 16 AND 24 - 34. THE AVERAGE RMSD'S BETWEEN THE 23 REFINED STRUCTURES AND AVERAGE STRUCTURE ARE AS FOLLOWS: 0.81 (RESIDUES 4 - 16 AND 24 - 34, BACKBONE ATOMS) 1.48 (RESIDUES 4 - 16 AND 24 - 34, HEAVY ATOMS) 1.08 (ALL BACKBONE ATOMS) 1.77 (ALL HEAVY ATOMS).
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 23

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