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Yorodumi- PDB-2y6n: STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y6n | |||||||||
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Title | STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE. | |||||||||
Components | VAL-GRAMICIDIN A | |||||||||
Keywords | ANTIBIOTIC / ION CHANNEL / MESOPHASE / SPONGE PHASE | |||||||||
Function / homology | GRAMICIDIN A / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | |||||||||
Authors | Hoefer, N. / Aragao, D. / Caffrey, M. | |||||||||
Citation | Journal: Cryst.Growth Des. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y6n.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y6n.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6n ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6n | HTTPS FTP |
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-Related structure data
Related structure data | 2y5mSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 | Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 6 / 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 #2: Chemical | #3: Chemical | ChemComp-P4C / | #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: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % Description: DATA WERE COLLECTED USING A COLLIMATED MINIBEAM WITH A 10 MICRON BEAMSIZE |
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Crystal grow | Method: lipidic cubic phase Details: 30 %(W/V) POLYETHYLENE GLYCOL (PEG) 8000, 0.2 M NH4SO4, LIPIDIC CUBIC PHASE OF 8.8 MAG (SN-1-O-(CIS-8)HEXADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO 8.8 MAG. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Feb 22, 2009 / 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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→30.15 Å / Num. obs: 28320 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.26→1.29 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y5M Resolution: 1.26→30.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.027 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 15P A1016 IN THIS ENTRY WAS NAMED PEG-A IN THE PRIMARY CITATION. RESIDUES 15P A1017 AND 15P A1018 IN THIS ENTRY WERE NAMED PEG-B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 15P A1016 IN THIS ENTRY WAS NAMED PEG-A IN THE PRIMARY CITATION. RESIDUES 15P A1017 AND 15P A1018 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: 11.441 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→30.15 Å
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Refine LS restraints |
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