+Open data
-Basic information
Entry | Database: PDB / ID: 1alx | |||||||||
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Title | GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE) | |||||||||
Components | (GRAMICIDIN A) x 2 | |||||||||
Keywords | ANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / ABTIBIOTIC / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN | |||||||||
Function / homology | GRAMICIDIN D / METHANOL / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Burkhart, B.M. / Langs, D.A. / Smith, G.D. / Courseille, C. / Precigoux, G. / Hospital, M. / Pangborn, W.A. / Duax, W.L. | |||||||||
Citation | Journal: Biophys.J. / Year: 1998 Title: Heterodimer Formation and Crystal Nucleation of Gramicidin D Authors: Burkhart, B.M. / Gassman, R.M. / Langs, D.A. / Pangborn, W.A. / Duax, W.L. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Monoclinic Uncomplexed Double-Stranded, Antiparallel, Left-Handed Beta 5.6-Helix (Increases Decreases Beta 5.6) Structure of Gramicidin A: Alternate Patterns of Helical Association and Deformation Authors: Langs, D.A. / Smith, G.D. / Courseille, C. / Precigoux, G. / Hospital, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1alx.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1alx.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 1alx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1alx ftp://data.pdbj.org/pub/pdb/validation_reports/al/1alx | HTTPS FTP |
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-Related structure data
Related structure data | 1al4C 1alzC 1gma C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.96861, 0.1753, -0.17624), Vector: |
-Components
#1: Protein/peptide | Type: Polypeptide / Class: Antibiotic / Mass: 1859.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: GRAMICIDIN D IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 1). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16). Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN D | ||
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#2: Protein/peptide | Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: GRAMICIDIN D IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 1). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16). Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN D | ||
#3: Chemical | ChemComp-MOH / Compound details | GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 25.57 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN METHANOL., PH 7.0, BATCH METHOD | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 1, 1990 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→100 Å / Num. obs: 7726 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 1 % / Net I/σ(I): 85.41 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 1 % / Mean I/σ(I) obs: 35.53 / % possible all: 99 |
Reflection | *PLUS Rmerge(I) obs: 0.0891 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GMA 1gma Resolution: 1.2→100 Å / Num. parameters: 3422 / Num. restraintsaints: 5704 / Cross valid method: FREE R-VALUE / σ(F): 0 StereochEM target val spec case: MODIFIED ENGH AND HUBER FOR ETHANOLAMINE BASED ON SERINE Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER (G = 0.12792 U = 0.82322) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 367.54 / Occupancy sum non hydrogen: 315.41 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.1 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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