BMRB Entry 34121
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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/BMR34121
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Title: NMR solution structure of lysostaphin PubMed: 30018958
Deposition date: 2017-04-07 Original release date: 2018-05-10
Authors: Tossavainen, H.; Raulinaitis, V.; Permi, P.
Citation: Tossavainen, Helena; Raulinaitis, Vytas; Kauppinen, Linda; Pentikainen, Ulla; Maaheimo, Hannu; Permi, Perttu. "Structural and Functional Insights Into Lysostaphin-Substrate Interaction" Front. Mol. Biosci. 5, 60-60 (2018).
Assembly members:
entity_1, polymer, 245 residues, 26876.070 Da.
entity_ZN, non-polymer, 65.409 Da.
Natural source: Common Name: Staphylococcus simulans Taxonomy ID: 1286 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus simulans
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: GSHEHSAQWLNNYKKGYGYG
PYPLGINGGMHYGVDFFMNI
GTPVKAISSGKIVEAGWSNY
GGGNQIGLIENDGVHRQWYM
HLSKYNVKVGDYVKAGQIIG
WSGSTGYSTAPHLHFQRMVN
SFSNSTAQDPMPFLKSAGYG
KAGGTVTPTPNTGWKTNKYG
TLYKSESASFTPNTDIITRT
TGPFRSMPQSGVLKAGQTIH
YDEVMKQDGHVWVGYTGNSG
QRIYLPVRTWNKSTNTLGVL
WGTIK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 763 |
| 15N chemical shifts | 245 |
| 1H chemical shifts | 1614 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 245 residues - 26876.070 Da.
| 1 | GLY | SER | HIS | GLU | HIS | SER | ALA | GLN | TRP | LEU | ||||
| 2 | ASN | ASN | TYR | LYS | LYS | GLY | TYR | GLY | TYR | GLY | ||||
| 3 | PRO | TYR | PRO | LEU | GLY | ILE | ASN | GLY | GLY | MET | ||||
| 4 | HIS | TYR | GLY | VAL | ASP | PHE | PHE | MET | ASN | ILE | ||||
| 5 | GLY | THR | PRO | VAL | LYS | ALA | ILE | SER | SER | GLY | ||||
| 6 | LYS | ILE | VAL | GLU | ALA | GLY | TRP | SER | ASN | TYR | ||||
| 7 | GLY | GLY | GLY | ASN | GLN | ILE | GLY | LEU | ILE | GLU | ||||
| 8 | ASN | ASP | GLY | VAL | HIS | ARG | GLN | TRP | TYR | MET | ||||
| 9 | HIS | LEU | SER | LYS | TYR | ASN | VAL | LYS | VAL | GLY | ||||
| 10 | ASP | TYR | VAL | LYS | ALA | GLY | GLN | ILE | ILE | GLY | ||||
| 11 | TRP | SER | GLY | SER | THR | GLY | TYR | SER | THR | ALA | ||||
| 12 | PRO | HIS | LEU | HIS | PHE | GLN | ARG | MET | VAL | ASN | ||||
| 13 | SER | PHE | SER | ASN | SER | THR | ALA | GLN | ASP | PRO | ||||
| 14 | MET | PRO | PHE | LEU | LYS | SER | ALA | GLY | TYR | GLY | ||||
| 15 | LYS | ALA | GLY | GLY | THR | VAL | THR | PRO | THR | PRO | ||||
| 16 | ASN | THR | GLY | TRP | LYS | THR | ASN | LYS | TYR | GLY | ||||
| 17 | THR | LEU | TYR | LYS | SER | GLU | SER | ALA | SER | PHE | ||||
| 18 | THR | PRO | ASN | THR | ASP | ILE | ILE | THR | ARG | THR | ||||
| 19 | THR | GLY | PRO | PHE | ARG | SER | MET | PRO | GLN | SER | ||||
| 20 | GLY | VAL | LEU | LYS | ALA | GLY | GLN | THR | ILE | HIS | ||||
| 21 | TYR | ASP | GLU | VAL | MET | LYS | GLN | ASP | GLY | HIS | ||||
| 22 | VAL | TRP | VAL | GLY | TYR | THR | GLY | ASN | SER | GLY | ||||
| 23 | GLN | ARG | ILE | TYR | LEU | PRO | VAL | ARG | THR | TRP | ||||
| 24 | ASN | LYS | SER | THR | ASN | THR | LEU | GLY | VAL | LEU | ||||
| 25 | TRP | GLY | THR | ILE | LYS |
Entity 2, entity_2 - Zn - 65.409 Da.
| 1 | ZN |
Samples:
sample_1: lysostaphin, [U-13C; U-15N], 0.36 mM; Bis-Tris 20 mM; ZnCl2 0.36 mM
sample_2: lysostaphin, [U-13C; U-15N], 0.47 mM; Bis-Tris 20 mM; ZnCl2 0.36 mM
sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 308 K
sample_conditions_2: ionic strength: 0.15 M; 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 HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | 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 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_2 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_2 |
| 3D 1H-13C NOESY aromatic | sample_2 | isotropic | sample_conditions_2 |
Software:
VNMR, Varian - collection, processing
SPARKY, Goddard - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
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