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Yorodumi- PDB-2lbt: Solution structure of the C domain of RV0899(D236A) from mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lbt | ||||||
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Title | Solution structure of the C domain of RV0899(D236A) from mycobacterium tuberculosis | ||||||
Components | Uncharacterized protein Rv0899/MT0922 | ||||||
Keywords | peptidoglycan-binding protein / peptidoglycan / OmpATb | ||||||
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 / molecular dynamics | ||||||
Model details | lowest energy, model 20 | ||||||
Authors | Yao, Y. / Marassi, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Molecular Structure and Peptidoglycan Recognition of Mycobacterium tuberculosis ArfA (Rv0899). Authors: Yao, Y. / Barghava, N. / Kim, J. / Niederweis, M. / Marassi, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lbt.cif.gz | 716.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lbt.ent.gz | 603.3 KB | Display | PDB format |
PDBx/mmJSON format | 2lbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lbt_validation.pdf.gz | 535.7 KB | Display | wwPDB validaton report |
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Full document | 2lbt_full_validation.pdf.gz | 808.2 KB | Display | |
Data in XML | 2lbt_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 2lbt_validation.cif.gz | 87 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/2lbt ftp://data.pdbj.org/pub/pdb/validation_reports/lb/2lbt | HTTPS FTP |
-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: 14052.704 Da / Num. of mol.: 1 / Fragment: OmpA-like domain residues 196-326 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) / 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 | Contents: 0.5 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: protein-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | pH: 6.8 / Pressure: ambient / Temperature: 298 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: molecular dynamics / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 20 |