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- PDB-2xdc: Structure of linear gramicidin D obtained using Type I crystals g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xdc | |||||||||
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Title | Structure of linear gramicidin D obtained using Type I crystals grown in a lipid cubic phase. | |||||||||
![]() | GRAMICIDIN A | |||||||||
![]() | ANTIBIOTIC / ION CHANNEL / MONOOLEIN / LIPID CUBIC PHASE / MESOPHASE SPONGE PHASE / BILAYER / ANTIFUNGAL / ANTIBACTERIAL | |||||||||
Function / homology | GRAMICIDIN A / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hoefer, N. / Aragao, D. / Caffrey, M. | |||||||||
![]() | ![]() Title: Crystallizing Transmembrane Peptides in Lipidic Mesophases Authors: Hoefer, N. / Aragao, D. / Caffrey, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.9 KB | Display | ![]() |
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PDB format | ![]() | 29.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1al4S 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: 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) ![]() #2: Chemical | ChemComp-15P / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | 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: 2.53 Å3/Da / Density % sol: 51 % Description: DATA WERE COLLECTED USING A COLLIMATED MINIBEAM WITH A 10 MICRON BEAMSIZE. |
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Crystal grow | Method: lipidic cubic phase / pH: 9 Details: 20 %(W/V) POLYETHYLENE GLYCOL (PEG) 6000, 0.1 M BICINE, PH 9.0. LIPIDIC CUBIC PHASE OF MONOOLEIN WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO MONOOLEIN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 16, 2008 / Details: SI(111) DOUBLE CRYSTAL |
Radiation | Monochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03312 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.3 Å / Num. obs: 11779 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / % possible all: 80.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AL4 Resolution: 1.7→27.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.796 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.243 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27.15 Å
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Refine LS restraints |
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