+Open data
-Basic information
Entry | Database: PDB / ID: 1jo3 | |||||||||
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Title | Gramicidin B in Sodium Dodecyl Sulfate Micelles (NMR) | |||||||||
Components | GRAMICIDIN B | |||||||||
Keywords | ANTIBIOTIC / GRAMICIDIN / ANTIFUNGAL / ANTIBACTERIAL / MEMBRANE ION CHANNEL / LINEAR GRAMICIDIN / SDS MICELLES | |||||||||
Function / homology | GRAMICIDIN B / : Function and homology information | |||||||||
Biological species | BREVIBACILLUS BREVIS (bacteria) | |||||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION | |||||||||
Model type details | minimized average | |||||||||
Authors | Townsley, L.E. / Tucker, W.A. / Hinton, J.F. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structures of Gramicidins A, B, and C Incorporated Into Sodium Dodecyl Sulfate Micelles. Authors: Townsley, L.E. / Tucker, W.A. / Sham, S. / Hinton, J.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jo3.cif.gz | 19.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jo3.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jo3_validation.pdf.gz | 289.3 KB | Display | wwPDB validaton report |
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Full document | 1jo3_full_validation.pdf.gz | 289 KB | Display | |
Data in XML | 1jo3_validation.xml.gz | 1.9 KB | Display | |
Data in CIF | 1jo3_validation.cif.gz | 2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/1jo3 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/1jo3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: A 40MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED. |
-Sample preparation
Details | Contents: 5MM GRAMICIDIN B, 250MM DEUTERATED SODIUM DODECYL SULFATE, 80% 100MM PHOSPHATE BUFFER PH 6.5, 10% D2O, 10% DEUTERATED TFE |
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Sample conditions | pH: 6.5 / Pressure: AMBIENT / Temperature: 328 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian VXRS / Manufacturer: Varian / Model: VXRS / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION Software ordinal: 1 Details: THE STRUCTURE WAS MODELED USING 622 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS ...Details: THE STRUCTURE WAS MODELED USING 622 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 TO EMULATE THAT OF THE MICELLE INTERIOR. | |||||||||||||||
NMR representative | Selection criteria: minimized average structure | |||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |