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- PDB-1ohm: Sakacin P variant that is structurally stabilized by an inserted ... -
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Open data
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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. | ||||||
![]() | BACTERIOCIN SAKACIN P | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING | ||||||
![]() | Uteng, M. / Hauge, H.H. / Markwick, P.R. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J. / Muhle-Goll, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.7 KB | Display | ![]() |
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PDB format | ![]() | 100.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 353.6 KB | Display | ![]() |
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Full document | ![]() | 410.2 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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. |
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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 |