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- PDB-3f2f: Crystal structure of the mercury-bound form of MerB, the Organome... -

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Basic information

Entry
Database: PDB / ID: 3f2f
TitleCrystal structure of the mercury-bound form 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: 1.98 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)46,5985
Polymers46,1172
Non-polymers4813
Water4,071226
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2592
Polymers23,0581
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3393
Polymers23,0581
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.108, 88.836, 51.584
Angle α, β, γ (deg.)90.00, 100.56, 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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-BR / BROMIDE ION


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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.86 Å3/Da / Density % sol: 33.92 %
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: 1.97→25 Å / Num. obs: 45866 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.04 Å2 / Rsym value: 0.105
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.41 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data 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: 1.98→24.38 Å / SU ML: 0.25 / σ(F): 0.02 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 3845 8.59 %
Rwork0.173 --
obs0.176 44750 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.01 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3841 Å20 Å21.73 Å2
2---0.2542 Å2-0 Å2
3----0.1299 Å2
Refinement stepCycle: LAST / Resolution: 1.98→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 3 226 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d03160
X-RAY DIFFRACTIONf_angle_d0.994309
X-RAY DIFFRACTIONf_dihedral_angle_d15.491115
X-RAY DIFFRACTIONf_chiral_restr0.06511
X-RAY DIFFRACTIONf_plane_restr0552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00520.20541020.17521137X-RAY DIFFRACTION70
2.0052-2.03160.23341350.16041397X-RAY DIFFRACTION94
2.0316-2.05940.24371390.16521491X-RAY DIFFRACTION94
2.0594-2.08880.23841410.171491X-RAY DIFFRACTION95
2.0888-2.120.21071450.1691507X-RAY DIFFRACTION95
2.12-2.15310.26671390.16441480X-RAY DIFFRACTION95
2.1531-2.18830.2471370.17741461X-RAY DIFFRACTION96
2.1883-2.2260.2121520.16961547X-RAY DIFFRACTION96
2.226-2.26650.23181420.16131471X-RAY DIFFRACTION96
2.2665-2.31010.19481450.15921526X-RAY DIFFRACTION97
2.3101-2.35720.22851430.16691529X-RAY DIFFRACTION97
2.3572-2.40840.22551430.16931516X-RAY DIFFRACTION98
2.4084-2.46440.22551450.17731534X-RAY DIFFRACTION98
2.4644-2.52590.23621430.17951561X-RAY DIFFRACTION97
2.5259-2.59410.22471420.18341514X-RAY DIFFRACTION98
2.5941-2.67040.25771470.17541561X-RAY DIFFRACTION99
2.6704-2.75650.24531380.19261542X-RAY DIFFRACTION99
2.7565-2.85480.25531460.18531551X-RAY DIFFRACTION99
2.8548-2.9690.23251470.18281561X-RAY DIFFRACTION99
2.969-3.10380.21761440.17011556X-RAY DIFFRACTION100
3.1038-3.26710.20241470.16461569X-RAY DIFFRACTION100
3.2671-3.47130.1821490.16271572X-RAY DIFFRACTION100
3.4713-3.73840.19751450.16261554X-RAY DIFFRACTION100
3.7384-4.1130.18241500.15251571X-RAY DIFFRACTION100
4.113-4.70440.19261500.15821588X-RAY DIFFRACTION100
4.7044-5.91310.19371460.17971544X-RAY DIFFRACTION100
5.9131-24.38320.21430.19041574X-RAY DIFFRACTION100

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