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Yorodumi- PDB-2n01: NMR structure of VirB9 C-terminal domain in complex with VirB7 N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n01 | ||||||
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Title | NMR structure of VirB9 C-terminal domain in complex with VirB7 N-terminal domain from Xanthomonas citri's T4SS | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/PROTEIN TRANSPORT / T4SS / lipoprotein / protein-peptide complex / VirB9 / VirB7 / PROTEIN TRANSPORT-PROTEIN TRANSPORT complex | ||||||
Function / homology | Function and homology information Immunoglobulin-like - #2500 / Toxin co-regulated pilus biosynthesis protein Q, C-terminal / Toxin co-regulated pilus biosynthesis protein Q / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, water refinement in cartesian space | ||||||
Authors | Oliveira, L.C. / Souza, D.P. / Salinas, R.K. / Wienk, H. / Boelens, R. / Farah, S.C. | ||||||
Citation | Journal: Structure / Year: 2016 Title: VirB7 and VirB9 Interactions Are Required for the Assembly and Antibacterial Activity of a Type IV Secretion System. Authors: Oliveira, L.C. / Souza, D.P. / Oka, G.U. / Lima, F.D. / Oliveira, R.J. / Favaro, D.C. / Wienk, H. / Boelens, R. / Farah, C.S. / Salinas, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n01.cif.gz | 813.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n01.ent.gz | 680.7 KB | Display | PDB format |
PDBx/mmJSON format | 2n01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2n01_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 2n01_full_validation.pdf.gz | 608.3 KB | Display | |
Data in XML | 2n01_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2n01_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/2n01 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/2n01 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2665.913 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 24-46) / Source method: obtained synthetically Source: (synth.) Xanthomonas axonopodis pv. citri (bacteria) References: UniProt: Q8PJB3 |
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#2: Protein | Mass: 12471.122 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 154-255) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria) Strain: 306 / Gene: virB9, XAC2620, XAC2622 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PJB5 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.500 mM [U-99% 13C; U-99% 15N] Xac_VirB9CT, 1 mM Xac_VirB7NT, 20 mM [U-100% 2H] sodium acetate, 50 mM sodium chloride, 1 % sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.07 / pH: 5 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, water refinement in cartesian space Software ordinal: 1 Details: RECALCULATION USING RECOORD SCRIPTS, WATER REFINEMENT USING RECOORD SCRIPTS | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2216 / NOE intraresidue total count: 535 / NOE long range total count: 767 / NOE medium range total count: 239 / NOE sequential total count: 675 / Hydrogen bond constraints total count: 78 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 70 / Protein psi angle constraints total count: 70 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.285 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0143283 Å |