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Yorodumi- PDB-3zq8: STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zq8 | |||||||||
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Title | STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A monovaccenin LIPID CUBIC PHASE | |||||||||
Components | VAL-GRAMICIDIN A | |||||||||
Keywords | ANTIBIOTIC / ION CHANNEL / MESOPHASE | |||||||||
Function / homology | GRAMICIDIN A / MONOVACCENIN / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Hoefer, N. / Aragao, D. / Caffrey, M. | |||||||||
Citation | Journal: To be Published Title: Crystallization of Gramicidin from a Monovaccenin Lipidic Cubic Phase Authors: Hoefer, N. / Aragao, D. / Caffrey, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zq8.cif.gz | 27.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zq8.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zq8_validation.pdf.gz | 961 KB | Display | wwPDB validaton report |
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Full document | 3zq8_full_validation.pdf.gz | 958 KB | Display | |
Data in XML | 3zq8_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 3zq8_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zq8 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zq8 | HTTPS FTP |
-Related structure data
Related structure data | 2xdcS S: Starting model for refinement |
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Similar structure data |
-Links
-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: (-0.99382, -0.08023, -0.07677), Vector: |
-Components
#1: Protein/peptide | Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 4 / 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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40.6 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 8.5 Details: 1M LITHIUM SULFATE, 10 MM NICKEL CHLORIDE, 0.1 M TRIS HCL, PH 8.5, LIPIDIC CUBIC PHASE OF MONOVACCENIN (11.7 MAG) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2009 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: CHANNEL-CUT DOUBLE-CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→22.9 Å / Num. obs: 6612 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5 / % possible all: 78.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XDC Resolution: 1.7→22.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.924 / SU B: 1.994 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / 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: 17.281 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→22.88 Å
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Refine LS restraints |
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