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- PDB-3f0o: Crystal structure of MerB, the Organomercurial Lyase involved in ... -

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Basic information

Entry
Database: PDB / ID: 3f0o
TitleCrystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system
ComponentsAlkylmercury lyase
KeywordsLYASE / merb / organomercurial lyase / alkylmercury lyase / mercury resistance / Mercuric resistance / Plasmid
Function / homology
Function and homology information


alkylmercury lyase / alkylmercury lyase activity / : / response to mercury ion
Similarity search - Function
Beta-Lactamase - #410 / Alkylmercury lyase, helix-turn-helix domain / Helix-turn-helix domain of alkylmercury lyase / Alkylmercury lyase / Alkylmercury lyase / Beta-Lactamase / Winged helix DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLafrance-Vanasse, J. / Lefebvre, M. / Di Lello, P. / Sygusch, J. / Omichinski, J.G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION
Authors: Lafrance-Vanasse, J. / Lefebvre, M. / Di Lello, P. / Sygusch, J. / Omichinski, J.G.
History
DepositionOct 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkylmercury lyase
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1963
Polymers46,1172
Non-polymers801
Water6,251347
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1382
Polymers23,0581
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase


Theoretical massNumber of molelcules
Total (without water)23,0581
Polymers23,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.710, 89.947, 52.167
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alkylmercury lyase / / Organomercurial lyase


Mass: 23058.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 296 K / pH: 5.5
Details: 20% polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0084
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0084 Å / Relative weight: 1
ReflectionResolution: 1.76→20 Å / Num. obs: 33974 / % possible obs: 97.9 % / Redundancy: 3.7 % / Rsym value: 0.05
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.181 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Preliminary protein model that is not in the PDB

Resolution: 1.76→19.67 Å / SU ML: 0.25 / σ(F): 0.07 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 1974 5.9 %
Rwork0.182 --
obs0.183 33441 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.42 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5188 Å2-0 Å20.8087 Å2
2---2.9854 Å20 Å2
3---1.4666 Å2
Refinement stepCycle: LAST / Resolution: 1.76→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 1 347 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053149
X-RAY DIFFRACTIONf_angle_d0.9744296
X-RAY DIFFRACTIONf_dihedral_angle_d14.9451112
X-RAY DIFFRACTIONf_chiral_restr0.065510
X-RAY DIFFRACTIONf_plane_restr0.005550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80510.28511170.21641904X-RAY DIFFRACTION82
1.8051-1.85390.26861390.20812186X-RAY DIFFRACTION93
1.8539-1.90840.21491350.19552148X-RAY DIFFRACTION94
1.9084-1.96990.22231390.18082214X-RAY DIFFRACTION95
1.9699-2.04020.25281420.19012250X-RAY DIFFRACTION96
2.0402-2.12180.18941410.17662259X-RAY DIFFRACTION97
2.1218-2.21830.22381410.18112253X-RAY DIFFRACTION98
2.2183-2.33510.19751450.1752297X-RAY DIFFRACTION98
2.3351-2.48110.22571460.18442307X-RAY DIFFRACTION99
2.4811-2.67220.19761420.18862287X-RAY DIFFRACTION99
2.6722-2.94040.21791470.1882330X-RAY DIFFRACTION99
2.9404-3.3640.21841450.17732334X-RAY DIFFRACTION99
3.364-4.23130.17791470.15972336X-RAY DIFFRACTION100
4.2313-19.66720.18251480.17782362X-RAY DIFFRACTION99

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