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- PDB-5u7c: Crystal structure of the lead-bound form of MerB formed from diet... -

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Basic information

Entry
Database: PDB / ID: 5u7c
TitleCrystal structure of the lead-bound form of MerB formed from diethyllead.
ComponentsAlkylmercury lyase
KeywordsLYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / Mercury / Diethyllead
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
ACETATE ION / BROMIDE ION / DIETHYLLEAD DIBROMIDE / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)47,1657
Polymers46,1172
Non-polymers1,0485
Water5,368298
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6224
Polymers23,0581
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5423
Polymers23,0581
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.066, 88.675, 54.832
Angle α, β, γ (deg.)90.000, 98.310, 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-ZN7 / DIETHYLLEAD DIBROMIDE


Mass: 425.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10Br2Pb
#3: Chemical ChemComp-BR / BROMIDE ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
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 MME was used as a cryo-protectant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 35220 / % possible obs: 97 % / Redundancy: 3.3 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.75→46.281 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.2031 3908 5.68 %
Rwork0.1699 --
obs0.1717 35220 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.78 Å2 / Biso mean: 35.1785 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: final / Resolution: 1.75→46.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 17 298 3493
Biso mean--23.24 40.6 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013278
X-RAY DIFFRACTIONf_angle_d1.0484475
X-RAY DIFFRACTIONf_chiral_restr0.057528
X-RAY DIFFRACTIONf_plane_restr0.007576
X-RAY DIFFRACTIONf_dihedral_angle_d15.5711961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7503-1.77160.36111010.38061702180371
1.7716-1.79410.38611150.32291941205681
1.7941-1.81770.32591340.29922161229587
1.8177-1.84260.2831340.2712228236296
1.8426-1.86890.28221420.25582391253399
1.8689-1.89680.27491490.24432418256798
1.8968-1.92640.28771430.22432414255799
1.9264-1.9580.28191430.21462315245898
1.958-1.99180.22651460.1992402254899
1.9918-2.0280.21311420.19792383252599
2.028-2.0670.22681370.19442372250999
2.067-2.10920.25491480.19312392254099
2.1092-2.15510.24691420.18192373251599
2.1551-2.20520.22861430.17032397254099
2.2052-2.26030.19921450.16342416256199
2.2603-2.32140.19261420.15652346248899
2.3214-2.38970.21351450.16232421256699
2.3897-2.46690.21581400.16932366250699
2.4669-2.5550.19871430.16962376251999
2.555-2.65730.22831420.162368251099
2.6573-2.77830.21481470.16042406255399
2.7783-2.92470.21461420.17292377251997
2.9247-3.10790.21561450.16152348249398
3.1079-3.34780.18061400.16182333247398
3.3478-3.68460.16771410.15172344248597
3.6846-4.21740.18191400.13692359249997
4.2174-5.31230.1241410.1362298243996
5.3123-46.29710.19371360.16272290242695
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)
10.4731-0.4211-0.02940.8894-0.07871.737-0.0214-0.0024-0.05790.0868-0.03390.0749-0.0751-0.023-0.00070.1519-0.02120.00970.1317-0.01020.175810.3523-2.862635.7076
20.5243-0.12050.01630.8831-0.13521.6390.02470.0462-0.0033-0.012-0.0478-0.0029-0.0322-0.09470.00010.13670.0422-0.00210.21820.02230.18870.2736-6.11310.6905
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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