+Open data
-Basic information
Entry | Database: PDB / ID: 2ml9 | ||||||
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Title | Solution structure of YSCUCN in a micellar complex with SDS | ||||||
Components | Yop proteins translocation protein U | ||||||
Keywords | MEMBRANE PROTEIN / YERSINIA / TYPE III SECRETION SYSTEM / YSCU / SECRETION SPECIFICITY / SODIUM DODECYL SULFATE | ||||||
Function / homology | Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / protein secretion / : / membrane => GO:0016020 / plasma membrane / Yop proteins translocation protein U Function and homology information | ||||||
Biological species | Yersinia pseudotuberculosis IP 32953 (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Weise, C.F. / Wolf-Watz, M. | ||||||
Citation | Journal: Biophys.J. / Year: 2014 Title: Negatively charged lipid membranes promote a disorder-order transition in the Yersinia YscU protein. Authors: Weise, C.F. / Login, F.H. / Ho, O. / Grobner, G. / Wolf-Watz, H. / Wolf-Watz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ml9.cif.gz | 377.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ml9.ent.gz | 330.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ml9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/2ml9 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/2ml9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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: 6832.867 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 211-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria) Gene: pYV0074, yscU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P69987 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 100 uM [U-99% 13C; U-99% 15N] protein-1, 30 mM sodium phosphate-2, 50 mM sodium chloride-3, 26 mM SDS-4, 92% H2O/8% D2O Solvent system: 92% H2O/8% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.12 / pH: 6.0 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: SIMULATED ANNEALING FROM EXTENDED STRUCTURE, MINIMIZATION IN TORSION ANGLE/CARTESIAN SPACE | |||||||||||||||||||||
NMR constraints | NOE constraints total: 203 / NOE intraresidue total count: 39 / NOE long range total count: 0 / NOE medium range total count: 45 / NOE sequential total count: 119 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 80 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0 ° Conformer selection criteria: structures with least restraint violations, followed by selection by lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum distance constraint violation: 0.554 Å / Maximum lower distance constraint violation: 0.073 Å / Maximum torsion angle constraint violation: 2.29 ° / Maximum upper distance constraint violation: 0 Å / Representative conformer: 1 | |||||||||||||||||||||
NMR ensemble rms | Dihedral angles rms dev error: 0.53 ° / Distance rms dev: 0 Å / Distance rms dev error: 0 Å |