BMRB Entry 25512
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25512
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: NMR structure of VirB9 C-terminal domain in complex with VirB7 N-terminal domain from Xanthomonas citri's T4SS. PubMed: 27594685
Deposition date: 2015-03-03 Original release date: 2015-09-10
Authors: Oliveira, Luciana; Souza, Diorge; Salinas, Roberto; Wienk, Hans; Boelens, Rolf; Farah, Shaker
Citation: Oliveira, Luciana Coutinho; Souza, Diorge Paulo; Oka, Gabriel Umaji; Lima, Filipe da Silva; Oliveira, Ronaldo Junio; Favaro, Denize Cristina; Wienk, Hans; Boelens, Rolf; Farah, Chuck Shaker; Salinas, Roberto Kopke. "VirB7 and VirB9 Interactions Are Required for the Assembly and Antibacterial Activity of a Type IV Secretion System" Structure 24, 1707-1718 (2016).
Assembly members:
Xac_VirB7NT, polymer, 24 residues, 2641.898 Da.
Xac_VirB9CT, polymer, 107 residues, 12471.240 Da.
Natural source: Common Name: g-proteobacteria Taxonomy ID: 190486 Superkingdom: Bacteria Kingdom: not available Genus/species: Xanthomonas citri
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
Xac_VirB7NT: XTKPAPDFGGRWKHVNHFDE
APTE
Xac_VirB9CT: GSHMNAKILKDRRYYYDYDY
ATRTKKSWLIPSRVYDDGKF
TYINMDLTRFPTGNFPAVFA
REKEHAEDFLVNTTVEGNTL
IVHGTYPFLVVRHGDNVVGL
RRNKQKX
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 470 |
| 15N chemical shifts | 114 |
| 1H chemical shifts | 860 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Xac_VirB7NT | 1 |
| 2 | Xac_VirB9CT | 2 |
Entities:
Entity 1, Xac_VirB7NT 24 residues - 2641.898 Da.
Modification: Acetylation (N-Terminal); Amidation (C-Terminal).
| 1 | ACE | THR | LYS | PRO | ALA | PRO | ASP | PHE | GLY | GLY | ||||
| 2 | ARG | TRP | LYS | HIS | VAL | ASN | HIS | PHE | ASP | GLU | ||||
| 3 | ALA | PRO | THR | GLU |
Entity 2, Xac_VirB9CT 107 residues - 12471.240 Da.
The first four residues (GSHM) belong to the vector encoded sequence.
| 1 | GLY | SER | HIS | MET | ASN | ALA | LYS | ILE | LEU | LYS | ||||
| 2 | ASP | ARG | ARG | TYR | TYR | TYR | ASP | TYR | ASP | TYR | ||||
| 3 | ALA | THR | ARG | THR | LYS | LYS | SER | TRP | LEU | ILE | ||||
| 4 | PRO | SER | ARG | VAL | TYR | ASP | ASP | GLY | LYS | PHE | ||||
| 5 | THR | TYR | ILE | ASN | MET | ASP | LEU | THR | ARG | PHE | ||||
| 6 | PRO | THR | GLY | ASN | PHE | PRO | ALA | VAL | PHE | ALA | ||||
| 7 | ARG | GLU | LYS | GLU | HIS | ALA | GLU | ASP | PHE | LEU | ||||
| 8 | VAL | ASN | THR | THR | VAL | GLU | GLY | ASN | THR | LEU | ||||
| 9 | ILE | VAL | HIS | GLY | THR | TYR | PRO | PHE | LEU | VAL | ||||
| 10 | VAL | ARG | HIS | GLY | ASP | ASN | VAL | VAL | GLY | LEU | ||||
| 11 | ARG | ARG | ASN | LYS | GLN | LYS | NH2 |
Samples:
sample_1: Xac_VirB9CT, [U-99% 13C; U-99% 15N], 0.500 mM; Xac_VirB7NT 1 mM; D2O, [U-99% 2H], 10%; sodium acetate, [U-100% 2H], 20 mM; sodium chloride 50 mM; sodium azide 1%; H2O 90%
sample_conditions_1: ionic strength: 0.07 M; pH: 5; pressure: 1 atm; temperature: 310 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C 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 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D CCH TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N, 13C CNH-NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 13C15N filtered NOE | sample_1 | isotropic | sample_conditions_1 |
| 2D 13C,15N filtered TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HBCBCGCDHD | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N-edited NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C-edited NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HBCBCGCDCEHE | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
TALOS, Cornilescu, Delaglio and Bax - data analysis
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CcpNmr_Analysis v2.4.1, CCPN - data analysis
NMR spectrometers:
- Bruker Avance III 800 MHz
- Bruker Avance III 900 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts