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Yorodumi- PDB-1ywl: Solution NMR structure of the protein EF2693 from E. faecalis: No... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ywl | ||||||
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Title | Solution NMR structure of the protein EF2693 from E. faecalis: Northeast Structural Genomics Consortium target EFR36 | ||||||
Components | Hypothetical UPF0213 protein EF2693 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha and beta / Northeast Structural Genomics Consortium (NESG) / Protein Structure Initiative (PSI) | ||||||
Function / homology | GIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / 3-Layer(aba) Sandwich / Alpha Beta / UPF0213 protein EF_2693 Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics simulated annealing | ||||||
Authors | Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution NMR structure of the protein EF2693 from E. faecalis: Northeast Structural Genomics Consortium target EFR36 Authors: Swapna, G.V.T. / Bhattacharya, A. / Aramini, J.M. / Acton, T.B. / Ma, L. / Xiao, R. / Shastry, R. / Shih, L. / Cunningham, K.E. / 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 | 1ywl.cif.gz | 317.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ywl.ent.gz | 263.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ywl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ywl_validation.pdf.gz | 344.3 KB | Display | wwPDB validaton report |
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Full document | 1ywl_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 1ywl_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 1ywl_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/1ywl ftp://data.pdbj.org/pub/pdb/validation_reports/yw/1ywl | HTTPS FTP |
-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: 11502.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF2693 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q830S9 |
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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. Automatic backbone resonance assignments were made using AutoAssign. Side-chain assignments were made manually. Automatic ...Text: The structure was determined using triple-resonance NMR spectroscopy. Automatic backbone resonance assignments were made using AutoAssign. Side-chain assignments were made manually. Automatic NOE assignments were made using AutoStructure. Dihedral angle restraints were made using Hyper and Talos. The SPINS database software was used as an integrating agent. PSVS was used to validate structure quality. |
-Sample preparation
Details | Contents: 5% D2O, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, 5 % D20, 95 % H20 Solvent system: 5 % D20, 95 % H20 |
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Sample conditions | Ionic strength: 100 mM NaCl, 5 mM CaCl2 / pH: 6.5 / Pressure: 1 atm / 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: torsion angle dynamics simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 912 conformationally-restricting noe-derived distance restraints, 216 dihedral restraints and 54 hydrogen bond restraints. | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Structures with lowest energy / Conformers calculated total number: 56 / Conformers submitted total number: 10 |