+Open data
-Basic information
Entry | Database: PDB / ID: 1gmk | |||||||||
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Title | GRAMICIDIN/KSCN COMPLEX | |||||||||
Components | GRAMICIDIN AGramicidin | |||||||||
Keywords | ANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / DOUBLE HELIX | |||||||||
Function / homology | GRAMICIDIN A / : / METHANOL / THIOCYANATE ION / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Doyle, D.A. / Wallace, B.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal Structure of the Gramicidin/Potassium Thiocyanate Complex. Authors: Doyle, D.A. / Wallace, B.A. #1: Journal: Biophys.J. / Year: 1994 Title: The Structure of the Gramicidin/Kscn Complex Authors: Doyle, D.A. / Wallace, B.A. #2: Journal: Ann.N.Y.Acad.Sci. / Year: 1984 Title: Crystalline Ion Complexes of Gramicidin A Authors: Kimball, M.R. / Wallace, B.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gmk.cif.gz | 27.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gmk.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 1gmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gmk ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gmk | HTTPS FTP |
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-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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16). Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-SCN / #4: Chemical | ChemComp-MOH / Compound details | GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Description: DATA COLLECTED AT ROOM TEMPERATURE WITH CRYSTAL IN METHANOL. | ||||||||||||||||||||
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Crystal grow | Details: CRYSTALLIZED IN METHANOL | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 11, 1991 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 5476 / % possible obs: 73.3 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.0325 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: GRAMICIDIN/CSCL COMPLEX, THEN GRAMICIDIN/CSSCN COMPLEX, BOTH WITHOUT IONS Resolution: 2.5→10 Å / σ(F): 3 Details: THE LOW TEMPERATURE FACTORS OF ATOMS N OF SCN 1, 2, 3, AND 4 ARE PROBABLY DUE TO POSITIONAL DISORDER OF THE THIOCYANATE MOLECULE WITH THE RESULT THAT OCCASIONALLY THE HEAVY SULFUR ATOM IS ...Details: THE LOW TEMPERATURE FACTORS OF ATOMS N OF SCN 1, 2, 3, AND 4 ARE PROBABLY DUE TO POSITIONAL DISORDER OF THE THIOCYANATE MOLECULE WITH THE RESULT THAT OCCASIONALLY THE HEAVY SULFUR ATOM IS SITUATED CLOSE TO THE PRESENT LOCATION OF THE NITROGEN. TWO METHANOL MOLECULES, MOH 5 AND MOH 19, WERE PLACED IN DENSITIES THAT ARE BELIEVED TO BELONG TO COMBINED DISORDERED CONFORMATIONS OF TRP A 15 AND TRP C 9 (MOH 19), AND TRP D 15 AND TRP A 9 (MOH 5).
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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