+Open data
-Basic information
Entry | Database: PDB / ID: 1alz | ||||||||||||
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Title | GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE) | ||||||||||||
Components |
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Keywords | ANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN | ||||||||||||
Function / homology | GRAMICIDIN A / GRAMICIDIN C / ETHANOL / : / : Function and homology information | ||||||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / DIRECT METHODS, FOURIER RECYCLING / Resolution: 0.86 Å | ||||||||||||
Authors | Burkhart, B.M. / Pangborn, W.A. / Duax, W.L. / Langs, D.A. | ||||||||||||
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: Science / Year: 1988 Title: Three-Dimensional Structure at 0.86 A of the Uncomplexed Form of the Transmembrane Ion Channel Peptide Gramicidin A. Authors: Langs, D.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1alz.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1alz.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 1alz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1alz ftp://data.pdbj.org/pub/pdb/validation_reports/al/1alz | HTTPS FTP |
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-Related 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: (0.86723, 0.1584, 0.47203), Vector: |
-Components
#1: Protein/peptide | Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1873.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: GRAMICIDIN C 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: NOR00248, GRAMICIDIN C | ||||||
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#2: Protein/peptide | Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 1 / 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 | ||||||
#3: Chemical | ChemComp-EOH / #4: Water | ChemComp-HOH / | Compound details | GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN | Sequence details | THE SEQUENCE IS FOR THE MAJOR COMPONENT GRAMICIDIN C (QIL1 AND TRP11) WHILE THE MINOR COMPONENT ...THE SEQUENCE IS FOR THE MAJOR COMPONENT GRAMICIDIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN ETHANOL., 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: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1987 / 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: 0.86→100 Å / Num. obs: 21454 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 1.1 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 0.86→0.9 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.043 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.043 / % possible all: 93.6 |
Reflection | *PLUS Rmerge(I) obs: 0.1641 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS, FOURIER RECYCLING Resolution: 0.86→100 Å / Num. parameters: 3464 / Num. restraintsaints: 5742 / 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 = 0.22140 U = 1.29472) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 365.06 / Occupancy sum non hydrogen: 312.16 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.86→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.1618 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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