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Open data
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Basic information
Entry | Database: PDB / ID: 1alz | ||||||||||||
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Title | GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE) | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Burkhart, B.M. / Pangborn, W.A. / Duax, W.L. / Langs, D.A. | ||||||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.9 KB | Display | ![]() |
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PDB format | ![]() | 37.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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 ![]() |
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Components
#1: Protein/peptide | ![]() ![]() ![]() ![]() 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) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | ![]() ![]() ![]() ![]() 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) ![]() ![]() ![]() ![]() | ||||||
#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: ![]() |
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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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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![]() | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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