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Yorodumi- PDB-2hep: Solution NMR structure of the UPF0291 protein ynzC from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hep | ||||||
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Title | Solution NMR structure of the UPF0291 protein ynzC from Bacillus subtilis. Northeast Structural Genomics target SR384. | ||||||
Components | UPF0291 protein ynzC | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR384 / AUTOSTRUCTURE / Northeast Structural Genomics Consortium / PSI-1 / Protein Structure Initiative / NESG | ||||||
Function / homology | Protein of unknown function DUF896 / Bacterial protein of unknown function (DUF896) / Helix hairpin bin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / cytoplasm / UPF0291 protein YnzC Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Aramini, J.M. / Swapna, G.V.T. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. ...Aramini, J.M. / Swapna, G.V.T. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis Authors: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T. ...Authors: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hep.cif.gz | 277.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hep.ent.gz | 227.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hep_validation.pdf.gz | 342.8 KB | Display | wwPDB validaton report |
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Full document | 2hep_full_validation.pdf.gz | 457.7 KB | Display | |
Data in XML | 2hep_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 2hep_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/2hep ftp://data.pdbj.org/pub/pdb/validation_reports/he/2hep | 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: 9895.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ynzC / Plasmid: PET21, SR384-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: O31818 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple resonance NMR spectroscopy. AUTOASSIGN was used to obtain automatic backbone assignments from GFT peak lists. Side chain assignments were completed ...Text: The structure was determined using triple resonance NMR spectroscopy. AUTOASSIGN was used to obtain automatic backbone assignments from GFT peak lists. Side chain assignments were completed manually. Automatic NOESY assignment, as well as distance and hydrogen bond constraints were determined using AutoStructure. Dihedral angle constraints were determined using HYPER. Completeness of NMR assignments (excluding C-terminal LEHHHHHH tag): Backbone: 91.9%; Side chain: 78.3%; Aromatics, 100%: Stereospecific methyl, 87.5%. Final structure quality factors (for residues 1 to 42 only; PSVS 1.2), where ordered residues [S(PHI)+ S(PSI) > 1.8] comprise 5-20 and 23-40: (A) RMSD (ordered residues): BB, 0.9; heavy atom, 1.5. (B) Ramachandran statistics for ordered residues: Most favored, 96.4%, Additionally allowed, 3.6%, generously allowed, 0.0%, disallowed, 0.0%. (C) Procheck scores for ordered residues (Raw/Z-): PHI-PSI, 0.11/0.75; All, -0.12/-0.71. (D) Molprobity clash score (Raw/Z-): 14.69/-1.00. (E) RPF scores for goodness of fit to NOESY data (all residues): Recall, 0.952, Precision, 0.839, F-measure, 0.892, DP-score, 0.628 |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 403 conformationally restricting NOE-derived distance constraints, 67 dihedral angle constraints, 42 hydrogen bond constraints, and 29 J(HN-Halpha) ...Details: The structures are based on a total of 403 conformationally restricting NOE-derived distance constraints, 67 dihedral angle constraints, 42 hydrogen bond constraints, and 29 J(HN-Halpha) coupling constants (12.5 constraints per residue; 1.1 long range constraints per residue; computed for residues 1 to 42 by PSVS 1.2). Structure determination was performed iteratively using AutoStructure (XPLOR-NIH). A final XPLOR calculation using the final constraints derived from AutoStructure was performed to yield the final structures. The unstructured C-terminal half of the molecule was included in all structural calculations but has been omitted from this deposition. Heteronuclear 15N,1H NOE experiments corroborate the presence of significant disorder in the C-terminal half of the protein (residues 43 to C-terminus). | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with lowest conformational energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |