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Yorodumi- PDB-2kgw: Solution Structure of the carboxy-terminal domain of OmpATb, a po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kgw | ||||||
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Title | Solution Structure of the carboxy-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis | ||||||
Components | Outer membrane protein A | ||||||
Keywords | MEMBRANE PROTEIN / outer membrane protein A / Mycobacterium tuberculosis / OmpA-like / Cell membrane / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information response to host pH environment / ammonium transmembrane transport / peptidoglycan binding / cell wall / response to acidic pH / porin activity / plasma membrane => GO:0005886 / monoatomic ion transport / peptidoglycan-based cell wall / cell outer membrane ...response to host pH environment / ammonium transmembrane transport / peptidoglycan binding / cell wall / response to acidic pH / porin activity / plasma membrane => GO:0005886 / monoatomic ion transport / peptidoglycan-based cell wall / cell outer membrane / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, minimization | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Yang, Y. / Auguin, D. / Delbecq, S. / Hoh, F. / Dumas, E. / Molle, V. / Saint, N. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall. Authors: Yang, Y. / Auguin, D. / Delbecq, S. / Dumas, E. / Molle, G. / Molle, V. / Roumestand, C. / Saint, N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kgw.cif.gz | 361.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kgw.ent.gz | 312.6 KB | Display | PDB format |
PDBx/mmJSON format | 2kgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/2kgw ftp://data.pdbj.org/pub/pdb/validation_reports/kg/2kgw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13082.653 Da / Num. of mol.: 1 Fragment: 13.1kDa carboxy-terminal Domain (198-326) of the carboxy-terminal (73-326) fragment of ompaTB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0899, MT0922, MTCY31.27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)omp8 / References: UniProt: P65593, UniProt: P9WIU5*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-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: DGSA-distance geometry simulated annealing, minimization Software ordinal: 1 / Details: Cyana, Amber | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |