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Yorodumi- PDB-1tkq: SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN A MEMBRA... -
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-Basic information
Entry | Database: PDB / ID: 1tkq | |||||||||
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Title | SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN A MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE IN THE PRESENCE OF CsCl | |||||||||
Components |
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Keywords | ANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN | |||||||||
Function / homology | MINI-GRAMICIDIN A - GRAMICIDIN A DIMER / SUCCINIC ACID / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Model type details | MINIMIZED AVERAGE | |||||||||
Authors | Xie, X. / Al-Momani, L. / Bockelmann, D. / Griesinger, C. / Koert, U. | |||||||||
Citation | Journal: FEBS J. / Year: 2005 Title: An Asymmetric Ion Channel Derived from Gramicidin A. Synthesis, Function and NMR Structure. Authors: Xie, X. / Al-Momani, L. / Reiss, P. / Griesinger, C. / Koert, U. #1: Journal: Science / Year: 1993 Title: High-Resolution Conformation of Gramicidin a in a Lipid Bilayer by Solid-State NMR Authors: Ketchem, R.R. / Hu, W. / Cross, T.A. #2: Journal: J.Mol.Biol. / Year: 1996 Title: Solution Structure of a Parallel Left-Handed Double-Helical Gramicidin-A Determined by 2D 1H NMR Authors: Chen, Y. / Tucker, A. / Wallace, B.A. #3: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2002 Title: Cation Control in Functional Helical Programming: Structures of a D,L-Peptide Ion Channel Authors: Arndt, H.-D. / Bockelmann, D. / Knoll, A. / Lamberth, S. / Griesinger, C. / Koert, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tkq.cif.gz | 17.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tkq.ent.gz | 14.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tkq_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
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Full document | 1tkq_full_validation.pdf.gz | 368.9 KB | Display | |
Data in XML | 1tkq_validation.xml.gz | 2.2 KB | Display | |
Data in CIF | 1tkq_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tkq ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tkq | 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 | Type: Polypeptide / Class: Antibiotic / Mass: 1470.798 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER. Source: (synth.) BREVIBACILLUS BREVIS (bacteria) References: NOR: NOR00243, MINI-GRAMICIDIN A - GRAMICIDIN A DIMER |
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#2: Protein/peptide | Type: Polypeptide / Class: Antibiotic / Mass: 1811.216 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER. Source: (synth.) BREVIBACILLUS BREVIS (bacteria) References: NOR: NOR00243, MINI-GRAMICIDIN A - GRAMICIDIN A DIMER |
#3: Chemical | ChemComp-SIN / Type: Polypeptide / Class: Antibiotic / Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 Details: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A HEAD-TO-HEAD MANNER. References: MINI-GRAMICIDIN A - GRAMICIDIN A DIMER |
Compound details | GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN |
Sequence details | BOTH OF THE C-TERMINI HAVE ETHANOLAMINE ATTACHED WITH THE CAPPING GROUP T-BUTYLDIPHENYLSILYL, WHICH ...BOTH OF THE C-TERMINI HAVE ETHANOLAMI |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: VARIABLE TEMPERATURE EXPERIMENTS WERE PERFORMED TO HAVE THE TEMPERATURE DEPENDENCE OF NH CHEMICAL SHIFTS, THEREFORE PROVIDE EVIDENCE FOR HYDROGEN BONDING. |
-Sample preparation
Details | Contents: 3MM SATURATED WITH CSCL |
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Sample conditions | Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 160 NOE- DERIVED DISTANCE CONSTRAINTS, 39 DIHEDRAL ANGLE RESTRAINTS, AND 40 DISTANCE RESTRAINTS FROM HYDROGEN BONDS | |||||||||
NMR ensemble | Conformer selection criteria: MINIMIZED AVERAGE STRUCTURE OF 11 STRUCTURES WITH THE LOWEST TARGET FUNCTION Conformers calculated total number: 50 / Conformers submitted total number: 1 |