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Yorodumi- PDB-1s6l: Solution structure of MerB, the Organomercurial Lyase involved in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6l | ||||||
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Title | Solution structure of MerB, the Organomercurial Lyase involved in the bacterial mercury resistance system | ||||||
Components | Alkylmercury lyase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information alkylmercury lyase / alkylmercury lyase activity / : / response to mercury ion Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / Simulated annealing, with a combination of torsion angle dynamics, cartesian dynamics | ||||||
Authors | Di Lello, P. / Benison, G.C. / Valafar, H. / Pitts, K.E. / Summers, A.O. / Legault, P. / Omichinski, J.G. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system. Authors: Di Lello, P. / Benison, G.C. / Valafar, H. / Pitts, K.E. / Summers, A.O. / Legault, P. / Omichinski, J.G. #1: Journal: J.Biomol.NMR / Year: 2004 Title: 1H, 15N, and 13C resonance assignment of the 23 kDa organomercurial lyase MerB in its free and mercury-bound forms Authors: Di Lello, P. / Benison, G.C. / Omichinski, J.G. / Legault, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s6l.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6l.ent.gz | 980.6 KB | Display | PDB format |
PDBx/mmJSON format | 1s6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6l ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6l | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 23058.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MERB / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase |
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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. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 10 mM sodium phosphate buffer and 10mM sodium chloride pH: 7.5 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
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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, with a combination of torsion angle dynamics, cartesian dynamics Software ordinal: 1 Details: The three-dimensional structures of MerB were determined using a set of 1493 NOE-derived distance restraints, 203 backbone dihedral angle (phi and psi) restraints, 5 chi angle restraints, 36 ...Details: The three-dimensional structures of MerB were determined using a set of 1493 NOE-derived distance restraints, 203 backbone dihedral angle (phi and psi) restraints, 5 chi angle restraints, 36 hydrogen-bond restraints and 298 one-bond residual dipolar coupling restraints. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: among the structures with the lowest rmsd to the minimized averge structure, the model with the lowest energy was selected | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: The submitted models are the 20 structures with no upper bound violation greater that 0.3 armstrongs and no dihedral angle restraint violation greater than 2 degrees and ...Conformer selection criteria: The submitted models are the 20 structures with no upper bound violation greater that 0.3 armstrongs and no dihedral angle restraint violation greater than 2 degrees and with the lowest energies. Conformers calculated total number: 55 / Conformers submitted total number: 20 |