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- PDB-3f0p: Crystal structure of the mercury-bound form of MerB, the Organome... -

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Basic information

Entry
Database: PDB / ID: 3f0p
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 / PHMBA / 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: 1.64 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 1.2Sep 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
Water5,603311
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)38.372, 89.203, 51.585
Angle α, β, γ (deg.)90.00, 100.48, 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.: 311 / 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: 1.88 Å3/Da / Density % sol: 34.66 %
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: 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: 1.64→20 Å / Num. obs: 40293 / % possible obs: 96.6 % / Redundancy: 3.9 % / Rsym value: 0.064
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.481 / % possible all: 93.2

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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 3F0O

3f0o


Resolution: 1.64→19.47 Å / SU ML: 0.18 / σ(F): 0.07 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1941 4.97 %
Rwork0.184 --
obs0.186 39084 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.2 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2576 Å20 Å21.1229 Å2
2---1.6032 Å20 Å2
3---0.3456 Å2
Refinement stepCycle: LAST / Resolution: 1.64→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 3 311 3395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063149
X-RAY DIFFRACTIONf_angle_d1.0494296
X-RAY DIFFRACTIONf_dihedral_angle_d15.8231112
X-RAY DIFFRACTIONf_chiral_restr0.067510
X-RAY DIFFRACTIONf_plane_restr0.005550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6820.23431200.22062281X-RAY DIFFRACTION81
1.682-1.72750.27031290.21792425X-RAY DIFFRACTION86
1.7275-1.77830.23041330.20232523X-RAY DIFFRACTION89
1.7783-1.83560.20211320.19012585X-RAY DIFFRACTION91
1.8356-1.90120.23981360.1882575X-RAY DIFFRACTION92
1.9012-1.97720.21761380.17912643X-RAY DIFFRACTION94
1.9772-2.06710.21811410.18362695X-RAY DIFFRACTION95
2.0671-2.1760.21851400.17442704X-RAY DIFFRACTION96
2.176-2.31210.21111430.18342734X-RAY DIFFRACTION97
2.3121-2.49030.23211420.18892745X-RAY DIFFRACTION97
2.4903-2.74030.18341460.19092782X-RAY DIFFRACTION98
2.7403-3.13540.22511450.18362786X-RAY DIFFRACTION98
3.1354-3.94490.19641470.16612805X-RAY DIFFRACTION99
3.9449-19.47450.18981490.1752860X-RAY DIFFRACTION99

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