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- PDB-2y5m: 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: 2y5m | |||||||||
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Title | STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE. | |||||||||
![]() | VAL-GRAMICIDIN A | |||||||||
![]() | ANTIBIOTIC / ION CHANNEL / MESOPHASE / SPONGE PHASE | |||||||||
Function / homology | GRAMICIDIN A / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hoefer, N. / Aragao, D. / Caffrey, M. | |||||||||
![]() | ![]() Title: Membrane Protein Crystallization in Lipidic Mesophases. Hosting Lipid Effects on the Crystallization and Structure of a Transmembrane Peptide Authors: Hoefer, N. / Aragao, D. / Lyons, J. / 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 | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 870.3 KB | Display | ![]() |
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Full document | ![]() | 872.6 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y6nC ![]() 1al4S S: Starting model for refinement C: citing same article ( |
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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 | #3: 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: 2.58 Å3/Da / Density % sol: 52.3 % Description: DATA WERE COLLECTED USING A COLLIMATED MINIBEAM WITH A 10 MICRON BEAMSIZE |
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Crystal grow | Method: lipidic cubic phase / pH: 5.5 Details: 25 %(W/V) PEG 3350, 0.2 M LISO4, 0.1 M BIS TRIS AT PH 5.5, LIPIDIC CUBIC PHASE OF 7.7 MAG (SN-1-O-(CIS-7)TETRADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Aug 5, 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: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→30.2 Å / Num. obs: 46435 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 65 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AL4 Resolution: 1.08→30.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.709 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 15P A1001 IN THIS ENTRY WAS NAMED PEG-A IN THE PRIMARY CITATION. RESIDUES 15P A1002 AND 15P A1003 IN THIS ENTRY WERE NAMED PEG-B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 15P A1001 IN THIS ENTRY WAS NAMED PEG-A IN THE PRIMARY CITATION. RESIDUES 15P A1002 AND 15P A1003 IN THIS ENTRY WERE NAMED PEG-B AND PEG-B' RESPECTIVELY IN THE PRIMARY CITATION.
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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: 12.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→30.2 Å
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Refine LS restraints |
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