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- PDB-3f2h: Crystal structure of the mercury-bound form of MerB mutant C160S,... -

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Basic information

Entry
Database: PDB / ID: 3f2h
TitleCrystal structure of the mercury-bound form 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
: / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6284
Polymers48,2272
Non-polymers4012
Water4,630257
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3142
Polymers24,1131
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3142
Polymers24,1131
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.880, 89.169, 54.627
Angle α, β, γ (deg.)90.00, 97.45, 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: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: X12B / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 22364 / % possible obs: 89.7 % / Redundancy: 3.5 % / Rsym value: 0.047
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 11.9 / Rsym value: 0.098 / % possible all: 98.5

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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: 2→19.3 Å / SU ML: 0.29 / σ(F): 0.04 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1967 8.92 %
Rwork0.191 --
obs0.196 22052 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.8 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1733 Å20 Å23.7824 Å2
2---3.0403 Å2-0 Å2
3----2.7058 Å2
Refinement stepCycle: LAST / Resolution: 2→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 2 257 3357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063162
X-RAY DIFFRACTIONf_angle_d1.014308
X-RAY DIFFRACTIONf_dihedral_angle_d16.1221114
X-RAY DIFFRACTIONf_chiral_restr0.064513
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05030.261460.1951517X-RAY DIFFRACTION93
2.0503-2.10570.23711520.18111565X-RAY DIFFRACTION98
2.1057-2.16750.25881600.17611612X-RAY DIFFRACTION98
2.1675-2.23740.24611060.19671099X-RAY DIFFRACTION90
2.2374-2.31720.2661680.1936662X-RAY DIFFRACTION81
2.3172-2.40990.26381570.19421610X-RAY DIFFRACTION99
2.4099-2.51930.25661560.1921611X-RAY DIFFRACTION100
2.5193-2.65180.25981590.1891607X-RAY DIFFRACTION100
2.6518-2.81750.23561590.20331625X-RAY DIFFRACTION100
2.8175-3.03430.26851600.20571625X-RAY DIFFRACTION100
3.0343-3.33820.24681580.19231618X-RAY DIFFRACTION100
3.3382-3.8180.22271000.19231022X-RAY DIFFRACTION63
3.818-4.7980.19691240.16861264X-RAY DIFFRACTION100
4.798-19.29910.21721620.18811648X-RAY DIFFRACTION99

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