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Yorodumi- PDB-1u2u: Nmr solution structure of a designed heterodimeric leucine zipper -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u2u | ||||||
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Title | Nmr solution structure of a designed heterodimeric leucine zipper | ||||||
Components | (General control protein GCN4) x 2 | ||||||
Keywords | TRANSCRIPTION / COILED COIL / LEUCINE ZIPPER / INTER-HELICAL ION PAIRING / ELECTROSTATIC INTERACTIONS | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, REGULARIZATION, SIMULATED ANNEALING, MOLECULAR DYNAMICS SIMULATION IN VACUO | ||||||
Authors | Marti, D.N. / Bosshard, H.R. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Inverse electrostatic effect: electrostatic repulsion in the unfolded state stabilizes a leucine zipper. Authors: Marti, D.N. / Bosshard, H.R. #1: Journal: J.Mol.Biol. / Year: 2003 Title: Electrostatic interactions in leucine zippers: thermodynamic analysis of the contributions of Glu and His residues and the effect of mutating salt bridges Authors: Marti, D.N. / Bosshard, H.R. #2: Journal: Biochemistry / Year: 2000 Title: Interhelical ion pairing in coiled coils: solution structure of a heterodimeric leucine zipper and determination of pKa values of Glu side chains Authors: Marti, D.N. / Jelesarov, I. / Bosshard, H.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u2u.cif.gz | 515.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u2u.ent.gz | 451.1 KB | Display | PDB format |
PDBx/mmJSON format | 1u2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u2u_validation.pdf.gz | 359.2 KB | Display | wwPDB validaton report |
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Full document | 1u2u_full_validation.pdf.gz | 679.2 KB | Display | |
Data in XML | 1u2u_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 1u2u_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u2u ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u2u | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3480.719 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic peptide based on the sequence of the leucine zipper domain in GCN4 (baker's yeast) |
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#2: Protein/peptide | Mass: 3508.238 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic peptide based on the sequence of the leucine zipper domain in GCN4 (baker's yeast) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: STRUCTURE WAS DETERMINED USING STANDARD 2D NMR TECHNIQUES |
-Sample preparation
Details | Contents: 2.6mM, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 10mM / pH: 5.7 / Pressure: AMBIENT / Temperature: 310.00 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, REGULARIZATION, SIMULATED ANNEALING, MOLECULAR DYNAMICS SIMULATION IN VACUO Software ordinal: 1 Details: STRUCTURES WERE CALCULATED ON THE BASIS OF 1246 NOE DERIVED DISTANCE CONSTRAINTS AND 44 PHI ANGLE RESTRAINTS | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, low deviation of experimental pKa values from pKa derived by continuum electrostatics ...Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, low deviation of experimental pKa values from pKa derived by continuum electrostatics calculations on structures Conformers calculated total number: 50 / Conformers submitted total number: 27 |