+Open data
-Basic information
Entry | Database: PDB / ID: 2mp8 | ||||||
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Title | NMR structure of NKR-5-3B | ||||||
Components | NKR-5-3B | ||||||
Keywords | ANTIMICROBIAL PROTEIN / bacteriocin / antimicrobial peptide / head-to-tail cyclic / helix bundle | ||||||
Function / homology | Bacteriocin AS-48 / Bacteriocin AS-48 / Circular bacteriocin / Bacteriocin class IId cyclical uberolysin-like / Bacteriocin As-48; Chain A / membrane => GO:0016020 / Up-down Bundle / Mainly Alpha / Nkr-5-3b Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Rosengren, K.J. / Craik, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium Authors: Himeno, K. / Rosengren, K.J. / Inoue, T. / Perez, R.H. / Colgrave, M.L. / Lee, H.S. / Chan, L.Y. / Henriques, S.T. / Fujita, K. / Ishibashi, N. / Zendo, T. / Wilaipun, P. / Nakayama, J. / ...Authors: Himeno, K. / Rosengren, K.J. / Inoue, T. / Perez, R.H. / Colgrave, M.L. / Lee, H.S. / Chan, L.Y. / Henriques, S.T. / Fujita, K. / Ishibashi, N. / Zendo, T. / Wilaipun, P. / Nakayama, J. / Leelawatcharamas, V. / Jikuya, H. / Craik, D.J. / Sonomoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mp8.cif.gz | 354.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mp8.ent.gz | 311 KB | Display | PDB format |
PDBx/mmJSON format | 2mp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/2mp8 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/2mp8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6340.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterococcus faecalis (bacteria) / Strain: NKR-5-3 / References: UniProt: A0A0M3KKS4*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR structure of a circular bacteriocin from Enterococcus faecium | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Structures generated by torsion angel dynamics and refined in explicit water using cartesian dynamics. | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1048 / NOE intraresidue total count: 297 / NOE long range total count: 183 / NOE medium range total count: 294 / NOE sequential total count: 274 / Hydrogen bond constraints total count: 96 / Protein chi angle constraints total count: 28 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.3 ° / Maximum upper distance constraint violation: 0.176 Å / Representative conformer: 1 |