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Yorodumi- PDB-2leg: Membrane protein complex DsbB-DsbA structure by joint calculation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2leg | ||||||
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Title | Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / OXIDOREDUCTASE / Disulfide bond / redox-active center / cell inner membrane / cell membrane / chaperone / electron transport / membrane / transmembrane / transport | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / ubiquinone binding / protein folding / outer membrane-bounded periplasmic space / response to heat / electron transfer activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Model details | closest to the average, model 8 | ||||||
Authors | Tang, M. / Sperling, L.J. / Berthold, D.A. / Schwieters, C.D. / Nesbitt, A.E. / Nieuwkoop, A.J. / Gennis, R.B. / Rienstra, C.M. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2011 Title: High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. Authors: Tang, M. / Sperling, L.J. / Berthold, D.A. / Schwieters, C.D. / Nesbitt, A.E. / Nieuwkoop, A.J. / Gennis, R.B. / Rienstra, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2leg.cif.gz | 1011.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2leg.ent.gz | 848.5 KB | Display | PDB format |
PDBx/mmJSON format | 2leg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2leg_validation.pdf.gz | 650.8 KB | Display | wwPDB validaton report |
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Full document | 2leg_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2leg_validation.xml.gz | 144.1 KB | Display | |
Data in CIF | 2leg_validation.cif.gz | 156.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/2leg ftp://data.pdbj.org/pub/pdb/validation_reports/le/2leg | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 21122.959 Da / Num. of mol.: 1 / Mutation: C33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEG4 |
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#2: Protein | Mass: 20106.982 Da / Num. of mol.: 1 / Mutation: C8A, C49V, C130S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbB, roxB, ycgA, b1185, JW5182 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6M2 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-UQ1 / |
-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Chemical shifts assignments and CC correlations provide dihedral angle and distance restraints. |
-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Joint calculation of DsbB-DsbA complex with solid-state NMR restraints and X-ray reflections from PDB entry 2HI7. | |||||||||||||||||||||
NMR constraints | NOE constraints total: 811 | |||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.51 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.52 Å | |||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.121 Å / Distance rms dev error: 0.003 Å |