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- PDB-1s6l: Solution structure of MerB, the Organomercurial Lyase involved in... -

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Basic information

Entry
Database: PDB / ID: 1s6l
TitleSolution structure of MerB, the Organomercurial Lyase involved in the bacterial mercury resistance system
ComponentsAlkylmercury lyase
KeywordsLYASE
Function / homology
Function and homology information


alkylmercury lyase / alkylmercury lyase activity / response to mercury ion
Similarity search - Function
Alkylmercury lyase / Alkylmercury lyase, helix-turn-helix domain / Helix-turn-helix domain of alkylmercury lyase / Alkylmercury lyase / : / Alkylmercury lyase / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Alkylmercury lyase / Alkylmercury lyase, helix-turn-helix domain / Helix-turn-helix domain of alkylmercury lyase / Alkylmercury lyase / : / Alkylmercury lyase / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Simulated annealing, with a combination of torsion angle dynamics, cartesian dynamics
AuthorsDi 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
DepositionJan 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkylmercury lyase


Theoretical massNumber of molelcules
Total (without water)23,0581
Polymers23,0581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 55The 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.
RepresentativeModel #1among the structures with the lowest rmsd to the minimized averge structure, the model with the lowest energy was selected

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Components

#1: Protein Alkylmercury lyase / Organomercurial lyase


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY-HSQC
121HNHA
1323D 13C-edited HMQC-NOESY
1424D 13C/13C-edited HMQC-NOESY-HMQC
1532D IPAP-[1H-15N] HSQC
1633D TROSY-based HNCO for measuraments of one-bond dipolar couplings
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-1.5mM MerB [U-15N], 10mM sodium phosphate buffer, 10mM sodium chloride, 7.5mM DTT, 1mM EDTA, 90%H2O, 10%D2O90% H2O/10% D2O
21.0-1.5mM MerB [U-13C and U-15N], 10mM sodium phosphate buffer, 10mM sodium chloride, 7.5mM DTT, 1mM EDTA, 99.9% D2O99.9% D2O
31.3mM MerB [U-13C and U-15N], 10mM sodium phosphate buffer, 10mM sodium chloride, 7.5mM DTT, 1mM EDTA, 11 mg/ml Pf1 phages, 90%H2O, 10%D2O90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate buffer and 10mM sodium chloride
pH: 7.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A.processing
PIPPGarrett, D.S., Powers, R., Gronenborn, A.M., Clore, G.M.data analysis
NMRView5.0.4Johnson, B.A. and Blevins, R.A.data analysis
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L.structure solution
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L.refinement
RefinementMethod: 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 representativeSelection criteria: among the structures with the lowest rmsd to the minimized averge structure, the model with the lowest energy was selected
NMR ensembleConformer 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

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