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Yorodumi- PDB-2m2j: Solution NMR structure of the N-terminal domain of STM1478 from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m2j | ||||||
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Title | Solution NMR structure of the N-terminal domain of STM1478 from Salmonella typhimurium LT2: Target STR147A of the Northeast Structural Genomics consortium (NESG), and APC101565 of the Midwest Center for Structural Genomics (MCSG). | ||||||
Components | Putative periplasmic proteinPeriplasm | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Northeast structural genomics consortium / MCSG / Midwest center for structural genomics / PSI-Biology | ||||||
Function / homology | Function and homology information YdgH protein / YdgH/BhsA/McbA-like domain / YdgH-like superfamily / YdgH/BhsA/McbA-like domain / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | SOLUTION NMR / restrained molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Houliston, S. / Yee, A. / Lemak, A. / Garcia, M. / Wu, B. / Savchenko, A. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO. Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. ...Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. / Ansong, C. / Xiao, R. / Acton, T.B. / Adkins, J.N. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. / Savchenko, A. / Szyperski, T. / Cort, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m2j.cif.gz | 414.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m2j.ent.gz | 342.3 KB | Display | PDB format |
PDBx/mmJSON format | 2m2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/2m2j ftp://data.pdbj.org/pub/pdb/validation_reports/m2/2m2j | HTTPS FTP |
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-Related structure data
Related structure data | 2ma4C 2ma8C 4evuC C: citing same article (ref.) |
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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: 10042.916 Da / Num. of mol.: 1 / Fragment: UNP residues 21-91 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: ydgH, STM1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZPL1 |
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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-13C; U-15N] protein, 10 mM BIS-TRIS, 200 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 1 mM benzamidine, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained 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: 100 / Conformers submitted total number: 20 |