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Yorodumi- PDB-1ohm: Sakacin P variant that is structurally stabilized by an inserted ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ohm | ||||||
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Title | Sakacin P variant that is structurally stabilized by an inserted C-terminal disulfide bridge. | ||||||
Components | BACTERIOCIN SAKACIN P | ||||||
Keywords | ANTIBIOTIC / PEDIOCIN-LIKE BACTERIOCINS / ANTIMICROBIAL PEPTIDES / SAKACIN ANTIBIOTIC / BACTERIOCIN | ||||||
Function / homology | Bacteriocin class IIa domain superfamily / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Class II bacteriocin / Bacteriocin class IIa family signature. / killing of cells of another organism / defense response to bacterium / extracellular region / Bacteriocin sakacin-P Function and homology information | ||||||
Biological species | LACTOBACILLUS SAKE (bacteria) | ||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING | ||||||
Authors | Uteng, M. / Hauge, H.H. / Markwick, P.R. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J. / Muhle-Goll, C. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Three-Dimensional Structure in Lipid Micelles of the Pediocin-Like Antimicrobial Peptide Sakacin P and a Sakacin P Variant that is Structurally Stabilized by an Inserted C-Terminal Disulfide Bridge Authors: Uteng, M. / Hauge, H.H. / Markwick, P.R. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J. / Muhle-Goll, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ohm.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ohm.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ohm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1ohm ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1ohm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4534.000 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE BRIDGE. Source: (gene. exp.) LACTOBACILLUS SAKE (bacteria) / Strain: LB790 / Variant: LB790/PGF10 / Plasmid: PGF10 / Production host: LACTOBACILLUS SAKE (bacteria) / Strain (production host): LB790 / Variant (production host): LB790/PGF10 / References: UniProt: P35618 |
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Compound details | ENGINEERED MUTATION IN CHAIN A: CYS 42 TO ASN 42 SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED ...ENGINEERED |
Sequence details | THE SEQUENCE IS DESCRIBED IN J. BACTERIOL. 182, 2643-2648 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: NOESY TOCSY |
NMR details | Text: THE STRUCTURES WERE DETERMINED USING A COMBINATION OF 1H NMR SPECTROSCOPIC METHODS FOLLOWED BY DISTANCE GEOMETRY/SIMULATED ANNEALING CALCULATIONS. |
-Sample preparation
Details | Contents: 250 MM DPC/10% D2O/ 0.1% TFA/1MM PEPTIDE |
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Sample conditions | pH: 2.8 / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1 Details: AMBER 6, SAN FRANCISCO, UNIVERSITY OF CALIFORNIA, 1999. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAIN VIOLATION AND OVERALL ENERGY Conformers calculated total number: 50 / Conformers submitted total number: 10 |