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- PDB-1qp6: SOLUTION STRUCTURE OF ALPHA2D -

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Entry
Database: PDB / ID: 1qp6
TitleSOLUTION STRUCTURE OF ALPHA2D
ComponentsPROTEIN (ALPHA2D)
KeywordsDE NOVO PROTEIN / DE NOVO DESIGN / PROTEIN DESIGN / PROTEIN FOLDING / BISECTING U MOTIF / FOUR-HELIX BUNDLE / HELIX-TURN-HELIX
MethodSOLUTION NMR / SIMULATED ANNEALING FOR 48 PS AT 2000K, A SLOW COOL TO 50K
AuthorsHill, R.B. / DeGrado, W.F.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Solution Structure of Alpha2D, A Nativelike De Novo Designed Protein
Authors: Hill, R.B. / DeGrado, W.F.
#1: Journal: J.Am.Chem.Soc. / Year: 1995
Title: A De Novo Designed Protein Mimics the Native State of Natural Proteins
Authors: Raleigh, D.P. / Betz, S.F. / Degrado, W.F.
History
DepositionJun 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ALPHA2D)
B: PROTEIN (ALPHA2D)


Theoretical massNumber of molelcules
Total (without water)8,5182
Polymers8,5182
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 60structures with the least restraint violations
RepresentativeModel #11lowest energy

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Components

#1: Protein/peptide PROTEIN (ALPHA2D)


Mass: 4258.936 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THIS SEQUENCE WAS DESIGNED TO FOLD INTO A HELIX-TURN-HELIX PEPTIDE THAT DIMERIZES TO FORM A FOUR-HELIX BUNDLE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131E-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES. BECAUSE ALPHA2D EXISTS AS A SYMMETRIC HOMODIMER, THERE EXISTS A PROBLEM OF DETERMINING WHETHER AN OBSERVED NOE ARISES FROM AN INTER- ...Text: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES. BECAUSE ALPHA2D EXISTS AS A SYMMETRIC HOMODIMER, THERE EXISTS A PROBLEM OF DETERMINING WHETHER AN OBSERVED NOE ARISES FROM AN INTER- OR INTRA- MONOMER CORRELATION. THIS PROBLEM WAS DEALT WITH AS DESCRIBED REMARK 3.

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Sample preparation

DetailsContents: 2 MM ALPHA2D TRIS, PH 7.3, 25 C
Sample conditionsIonic strength: 52 mM / pH: 7.3 / Pressure: AMBIENT / Temperature: 298.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: SIMULATED ANNEALING FOR 48 PS AT 2000K, A SLOW COOL TO 50K
Software ordinal: 1
Details: STRUCTURE BASED ON 834 RESTRAINTS: 140 LONG-RANGE RESTRAINTS, 30 PHI ANGLE RESTRAINTS, AND 14 CHI-1 ANGLE RESTRAINTS. 83 OF THE LONG-RANGE NOES (59%) WERE DETERMINED TO ARISE FROM INTER- ...Details: STRUCTURE BASED ON 834 RESTRAINTS: 140 LONG-RANGE RESTRAINTS, 30 PHI ANGLE RESTRAINTS, AND 14 CHI-1 ANGLE RESTRAINTS. 83 OF THE LONG-RANGE NOES (59%) WERE DETERMINED TO ARISE FROM INTER-MONOMER CORRELATIONS BY COMPUTATIONAL METHODS. THE OTHER NOES WERE TREATED USING A WEIGHTING FUNCTION DEVELOPED FOR SYMMMETRIC HOMODIMERS THAT ALLOWS EACH NOE TO ARISE FROM EITHER AN INTRA- OR INTER- MONOMER CORRELATIONS AS DESCRIBED BY NILGES, M. PROTEINS (1993) 17:297- 309. SYMMETRY TERMS WERE EMPLOYED FOR C-ALPHA CARBONS ONLY. SEE JACS(1998)120: 1138-1145 FOR MORE DETAILS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 16

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