BMRB Entry 30130
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30130
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Title: Identification and structural characterization of LytU PubMed: 28729697
Deposition date: 2016-07-06 Original release date: 2017-07-26
Authors: Raulinaitis, V.; Tossavainen, H.; Permi, P.
Citation: Raulinaitis, Vytas; Tossavainen, Helena; Aitio, Olli; Juuti, Jarmo; Hiramatsu, Keiichi; Kontinen, Vesa; Permi, Perttu. "Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family" Sci. Rep. 7, 6020-6020 (2017).
Assembly members:
entity_1, polymer, 145 residues, 16272.134 Da.
entity_ZN, non-polymer, 65.409 Da.
Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: GSKWEDFFRGSRITETFGKY
QHSPFDGKHYGIDFALPKGT
PIKAPTNGKVTRIFNNELGG
KVLQIAEDNGEYHQWYLHLD
KYNVKVGDRVKAGDIIAYSG
NTGIQTTGAHLHFQRMKGGV
GNAYAEDPKPFIDQLPDGER
SLYDL
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 474 |
| 15N chemical shifts | 138 |
| 1H chemical shifts | 981 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | ZINC ION | 2 |
Entities:
Entity 1, entity_1 145 residues - 16272.134 Da.
| 1 | GLY | SER | LYS | TRP | GLU | ASP | PHE | PHE | ARG | GLY | ||||
| 2 | SER | ARG | ILE | THR | GLU | THR | PHE | GLY | LYS | TYR | ||||
| 3 | GLN | HIS | SER | PRO | PHE | ASP | GLY | LYS | HIS | TYR | ||||
| 4 | GLY | ILE | ASP | PHE | ALA | LEU | PRO | LYS | GLY | THR | ||||
| 5 | PRO | ILE | LYS | ALA | PRO | THR | ASN | GLY | LYS | VAL | ||||
| 6 | THR | ARG | ILE | PHE | ASN | ASN | GLU | LEU | GLY | GLY | ||||
| 7 | LYS | VAL | LEU | GLN | ILE | ALA | GLU | ASP | ASN | GLY | ||||
| 8 | GLU | TYR | HIS | GLN | TRP | TYR | LEU | HIS | LEU | ASP | ||||
| 9 | LYS | TYR | ASN | VAL | LYS | VAL | GLY | ASP | ARG | VAL | ||||
| 10 | LYS | ALA | GLY | ASP | ILE | ILE | ALA | TYR | SER | GLY | ||||
| 11 | ASN | THR | GLY | ILE | GLN | THR | THR | GLY | ALA | HIS | ||||
| 12 | LEU | HIS | PHE | GLN | ARG | MET | LYS | GLY | GLY | VAL | ||||
| 13 | GLY | ASN | ALA | TYR | ALA | GLU | ASP | PRO | LYS | PRO | ||||
| 14 | PHE | ILE | ASP | GLN | LEU | PRO | ASP | GLY | GLU | ARG | ||||
| 15 | SER | LEU | TYR | ASP | LEU |
Entity 2, ZINC ION - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: Bis-Tris buffer 20 mM; LytU, [U-13C; U-15N], 0.5 mM
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 308 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCDCE)HE | sample_1 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCD)HD | sample_1 | isotropic | sample_conditions_1 |
Software:
AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
SPARKY, Goddard - chemical shift assignment
VNMRJ, Varian - collection
NMR spectrometers:
- Varian INOVA 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts