+Open data
-Basic information
Entry | Database: PDB / ID: 1qp6 | ||||||
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Title | SOLUTION STRUCTURE OF ALPHA2D | ||||||
Components | PROTEIN (ALPHA2D) | ||||||
Keywords | DE NOVO PROTEIN / DE NOVO DESIGN / PROTEIN DESIGN / PROTEIN FOLDING / BISECTING U MOTIF / FOUR-HELIX BUNDLE / HELIX-TURN-HELIX | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING FOR 48 PS AT 2000K, A SLOW COOL TO 50K | ||||||
Authors | Hill, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qp6.cif.gz | 373.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qp6.ent.gz | 327.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qp6 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qp6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | 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- ...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. |
-Sample preparation
Details | Contents: 2 MM ALPHA2D TRIS, PH 7.3, 25 C |
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Sample conditions | Ionic strength: 52 mM / pH: 7.3 / Pressure: AMBIENT / Temperature: 298.0 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 60 / Conformers submitted total number: 16 |