[English] 日本語
Yorodumi- PDB-2y5m: STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y5m | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE. | |||||||||
Components | VAL-GRAMICIDIN A | |||||||||
Keywords | ANTIBIOTIC / ION CHANNEL / MESOPHASE / SPONGE PHASE | |||||||||
Function / homology | GRAMICIDIN A / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2y5m.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2y5m.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y5m_validation.pdf.gz | 870.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2y5m_full_validation.pdf.gz | 872.6 KB | Display | |
Data in XML | 2y5m_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 2y5m_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5m ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5m | HTTPS FTP |
-Related structure data
Related structure data | 2y6nC 1al4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein/peptide | Type: Polypeptide / 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: Water | ChemComp-HOH / | Compound details | GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-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 |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.8266 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→30.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|