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Yorodumi- PDB-2ko6: Solution structure of protein sf3929 from Shigella flexneri 2a. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ko6 | ||||||
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Title | Solution structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929 | ||||||
Components | Uncharacterized protein yihD | ||||||
Keywords | Structural Genomics / Unknown function / alpha protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP | ||||||
Function / homology | Protein of unknown function DUF1040 / Protein of unknown function DUF1040 / YihD-like superfamily / Protein of unknown function (DUF1040) / Conserved Hypothetical Protein Ylqf; Chain: A; domain 2 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP) | ||||||
Citation | Journal: To be Published Title: Solution Structure of protein sf3929 from Shigella flexneri 2a. Northeast Structural Genomics Consortium target SfR81/Ontario Center for Structural Proteomics Target sf3929 Authors: Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Arrowsmith, C.H. #1: Journal: J.Biomol.Nmr / Year: 2011 Title: A novel strategy for NMR resonance assignment and protein structure determination. Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ko6.cif.gz | 571 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ko6.ent.gz | 479.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ko6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/2ko6 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/2ko6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 10321.919 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: yihD, S3818, SF3929 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83IV8, UniProt: A0A384LJ77*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Though residue F76-A83 forms a helice, the C-terminal part (residue 61 to residue 89) are in disorder status, no interaction with the core | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-100% 13C; U-100% 15N] sf3929, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / 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 |