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- PDB-3f2g: Crystal structure of MerB mutant C160S, the Organomercurial Lyase... -

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Basic information

Entry
Database: PDB / ID: 3f2g
TitleCrystal structure of MerB mutant C160S, 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 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 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkylmercury lyase
B: Alkylmercury lyase


Theoretical massNumber of molelcules
Total (without water)48,2272
Polymers48,2272
Non-polymers00
Water5,855325
1
A: Alkylmercury lyase


Theoretical massNumber of molelcules
Total (without water)24,1131
Polymers24,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase


Theoretical massNumber of molelcules
Total (without water)24,1131
Polymers24,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.835, 89.113, 54.722
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alkylmercury lyase / Organomercurial lyase


Mass: 24113.357 Da / Num. of mol.: 2 / Mutation: C160S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 296 K / pH: 5.5
Details: 6% polyethylene glycol 20000 MME and 6% polyethylene glycol 550 MME in 0.1 M sodium acetate pH 5.5 with 0.25 M sodium acetate., VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. obs: 32982 / % possible obs: 93.5 % / Redundancy: 3.5 % / Rsym value: 0.058
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.144 / % possible all: 92

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F0O

1f0o


Resolution: 1.781→24.68 Å / SU ML: 0.26 / σ(F): 0.07 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1943 6.05 %
Rwork0.185 --
obs0.188 32115 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.73 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8266 Å20 Å23.6097 Å2
2---3.4774 Å2-0 Å2
3----2.3492 Å2
Refinement stepCycle: LAST / Resolution: 1.781→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 0 325 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083218
X-RAY DIFFRACTIONf_angle_d1.1714389
X-RAY DIFFRACTIONf_dihedral_angle_d16.3191137
X-RAY DIFFRACTIONf_chiral_restr0.075521
X-RAY DIFFRACTIONf_plane_restr0.005563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.781-1.82560.26691260.20721974X-RAY DIFFRACTION84
1.8256-1.87490.28461360.20482129X-RAY DIFFRACTION91
1.8749-1.930.24851340.20852091X-RAY DIFFRACTION88
1.93-1.99230.22641400.19132155X-RAY DIFFRACTION93
1.9923-2.06350.22411520.18472331X-RAY DIFFRACTION98
2.0635-2.14610.23071500.17762320X-RAY DIFFRACTION98
2.1461-2.24370.25611230.19431897X-RAY DIFFRACTION80
2.2437-2.36190.26761180.1991824X-RAY DIFFRACTION77
2.3619-2.50970.25221490.19912355X-RAY DIFFRACTION100
2.5097-2.70330.22311530.18622371X-RAY DIFFRACTION100
2.7033-2.97490.21441520.18452371X-RAY DIFFRACTION100
2.9749-3.40440.20291530.17482358X-RAY DIFFRACTION100
3.4044-4.28560.21020.15791585X-RAY DIFFRACTION66
4.2856-24.67820.18851550.17592411X-RAY DIFFRACTION100

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