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Yorodumi- PDB-1ryk: Solution NMR Structure Protein yjbJ from Escherichia coli. Northe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ryk | |||||||||
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Title | Solution NMR Structure Protein yjbJ from Escherichia coli. Northeast Structural Genomics Consortium Target ET93; Ontario Centre for Structural Proteomics target EC0298_1_69; | |||||||||
Components | Protein yjbJ | |||||||||
Keywords | structural genomics / unknown function / Alpha protein / Protein Structure Initiative / OCSP / NESG / PSI / Northeast Structural Genomics Consortium | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing, restrained molecular dynamic simulations | |||||||||
Authors | Pineda-Lucena, A. / Liao, J. / Wu, B. / Yee, A. / Cort, J.R. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Citation | Journal: Proteins / Year: 2002 Title: An NMR approach to structural proteomics. Authors: Pineda-Lucena, A. / Liao, J. / Wu, B. / Yee, A. / Cort, J.R. / Kennedy, M.A. / Edwards, A.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 | 1ryk.cif.gz | 442.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ryk.ent.gz | 371.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ryk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ryk_validation.pdf.gz | 341.1 KB | Display | wwPDB validaton report |
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Full document | 1ryk_full_validation.pdf.gz | 484.4 KB | Display | |
Data in XML | 1ryk_validation.xml.gz | 26 KB | Display | |
Data in CIF | 1ryk_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/1ryk ftp://data.pdbj.org/pub/pdb/validation_reports/ry/1ryk | HTTPS FTP |
-Related structure data
Related structure data | 1jcuC 1jdqC 1je3C 1jrmC 1jw2C 1jw3C 1ryjC 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: 8339.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YJBJ, B4045, Z5644, ECS5028, SF4160, S3571 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P68206 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing, restrained molecular dynamic simulations Software ordinal: 1 Details: 2036 noe-derived distance constraints, 101 dihedral angle constraints, 62 hydrogen bonds | ||||||||||||||||
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 |