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Open data
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Basic information
Entry | Database: PDB / ID: 1al4 | |||||||||
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Title | GRAMICIDIN D FROM BACILLUS BREVIS (N-PROPANOL SOLVATE) | |||||||||
![]() | GRAMICIDIN D | |||||||||
![]() | ANTIBIOTIC / ANTIFUNGAL / ANTIBACTERIAL / LINEAR GRAMICIDIN / MEMBRANE ION CHANNEL | |||||||||
Function / homology | GRAMICIDIN D / N-PROPANOL / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Burkhart, B.M. / Gassman, R.M. / Pangborn, W.A. / Duax, W.L. | |||||||||
![]() | ![]() 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.7 KB | Display | ![]() |
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PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1alxC ![]() 1alzSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: (0.84724, 0.15064, 0.5094), Vector: |
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Components
#1: Protein/peptide | ![]() 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) ![]() #2: Chemical | ChemComp-POL / 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.15 % / Description: ISOMORPHOUS TO 1ALZ | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN N-PROPANOL, 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: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1996 / 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: 1.13→100 Å / Num. obs: 67561 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 47.6 |
Reflection shell | Resolution: 1.13→1.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 13.7 / Rsym value: 0.065 / % possible all: 82.4 |
Reflection | *PLUS Num. obs: 9572 / Num. measured all: 67561 |
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Processing
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Refinement | Method to determine structure: MOLECULAR PLACEMENT; DIFFERENCE MAPS Starting model: PDB ENTRY 1ALZ Resolution: 1.13→100 Å / Num. parameters: 3746 / Num. restraintsaints: 7423 / 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 = 0.5373 U = 0.7755) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 369.47 / Occupancy sum non hydrogen: 316.72 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.0851 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |