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- PDB-5u7a: Crystal structure of a complex formed between MerB and Dimethyltin -

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Basic information

Entry
Database: PDB / ID: 5u7a
TitleCrystal structure of a complex formed between MerB and Dimethyltin
ComponentsAlkylmercury lyase
KeywordsLYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / Mercury / Dimethyltin
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 / PHOSPHATE ION / Dimethyltin dibromide / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.532 Å
AuthorsWahba, H.M. / Stevenson, M. / Mansour, A. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon-Metal Bond Cleavage.
Authors: Wahba, H.M. / Stevenson, M.J. / Mansour, A. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,9096
Polymers46,1172
Non-polymers7924
Water4,972276
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5424
Polymers23,0581
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3672
Polymers23,0581
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.055, 88.648, 51.490
Angle α, β, γ (deg.)90.000, 100.340, 90.000
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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical ChemComp-ZN5 / Dimethyltin dibromide


Mass: 308.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6Br2Sn
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 1.85 Å3/Da / Density % sol: 33.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25% polyethylene glycol 2000 MME was used ...Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25% polyethylene glycol 2000 MME was used as a cryo-protectant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 43607 / % possible obs: 86.48 % / Redundancy: 3 % / Net I/σ(I): 16.45

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.532→43.98 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.62
RfactorNum. reflection% reflection
Rfree0.2105 3381 4.61 %
Rwork0.173 --
obs0.1748 43607 73.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.92 Å2 / Biso mean: 30.7102 Å2 / Biso min: 9.77 Å2
Refinement stepCycle: final / Resolution: 1.532→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 8 276 3462
Biso mean--20.78 33.88 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113248
X-RAY DIFFRACTIONf_angle_d1.3464430
X-RAY DIFFRACTIONf_chiral_restr0.052524
X-RAY DIFFRACTIONf_plane_restr0.008568
X-RAY DIFFRACTIONf_dihedral_angle_d15.7381158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5317-1.55360.4366190.290837739610
1.5536-1.57680.2916430.304688993222
1.5768-1.60150.2906630.28021207127031
1.6015-1.62770.3221750.25941580165540
1.6277-1.65580.30011020.2451920202248
1.6558-1.68590.26391090.23082164227356
1.6859-1.71830.26641290.22892595272464
1.7183-1.75340.26231470.21513040318778
1.7534-1.79150.20161550.20743263341882
1.7915-1.83320.23881560.20233356351284
1.8332-1.8790.21721610.19363349351085
1.879-1.92980.21591710.18653450362187
1.9298-1.98660.20311600.18133442360287
1.9866-2.05080.20241700.16693474364488
2.0508-2.1240.20531690.16553468363788
2.124-2.20910.22531670.17283478364588
2.2091-2.30960.20261700.16823503367389
2.3096-2.43140.20091700.1673559372990
2.4314-2.58370.23111680.17533560372890
2.5837-2.78320.2031710.17133592376390
2.7832-3.06320.24151730.18373610378392
3.0632-3.50630.18431740.16733655382992
3.5063-4.41690.19071780.14713691386993
4.4169-43.99840.19961810.15993791397296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5311-0.1648-0.00791.18360.27490.47290.0048-0.026-0.03980.1399-0.05960.08610.095-0.0564-0.00410.151-0.0230.02540.1281-0.00810.11249.2367-3.63433.433
20.7412-0.407-0.08041.5411-0.24230.47560.10320.14540.0007-0.1638-0.1272-0.0490.03070.0154-0.00150.12040.0272-0.01420.16510.01420.1092-0.9905-8.20279.7275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 208
2X-RAY DIFFRACTION2chain BB1 - 208

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