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- PDB-5u83: Crystal structure of a MerB-trimethytin complex. -

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Basic information

Entry
Database: PDB / ID: 5u83
TitleCrystal structure of a MerB-trimethytin complex.
ComponentsAlkylmercury lyase
KeywordsLYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / Mercury / trimethyltin
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 / Trimethyltin chloride / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.609 Å
AuthorsWahba, H.M. / Stevenson, M. / Mansour, A. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
National Science Foundation (NSF, United States) United States
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 13, 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 28, 2018Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,7137
Polymers46,1172
Non-polymers5975
Water8,377465
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3173
Polymers23,0581
Non-polymers2582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3964
Polymers23,0581
Non-polymers3383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.540, 89.072, 54.526
Angle α, β, γ (deg.)90.000, 98.650, 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-ZN8 / Trimethyltin chloride / Trimethyltin chloride


Mass: 199.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9ClSn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


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


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
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: 0.9724 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 45723 / % possible obs: 97 % / Redundancy: 3.5 % / Net I/σ(I): 17.92

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0P
Resolution: 1.609→33.586 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3869 4.37 %
Rwork0.159 84621 -
obs0.1608 88490 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.94 Å2 / Biso mean: 24.7003 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.609→33.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 23 465 3666
Biso mean--22.49 34 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113287
X-RAY DIFFRACTIONf_angle_d1.4014485
X-RAY DIFFRACTIONf_chiral_restr0.052528
X-RAY DIFFRACTIONf_plane_restr0.007577
X-RAY DIFFRACTIONf_dihedral_angle_d13.61173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6095-1.62910.2727930.24192064215766
1.6291-1.64970.27751060.24682274238071
1.6497-1.67140.27071100.22652484259478
1.6714-1.69430.29421220.20562670279285
1.6943-1.71850.22311280.20362805293388
1.7185-1.74420.21831340.20242945307992
1.7442-1.77140.24241430.20223126326998
1.7714-1.80050.24541410.1953105324698
1.8005-1.83150.21011480.18543205335399
1.8315-1.86480.22461450.17233106325199
1.8648-1.90070.24551430.16873128327199
1.9007-1.93950.20341490.15643184333399
1.9395-1.98160.19671410.158831373278100
1.9816-2.02770.16081450.152131993344100
2.0277-2.07840.18091430.15731153258100
2.0784-2.13460.21421450.160732033348100
2.1346-2.19740.21881480.152231603308100
2.1974-2.26830.2171420.147832163358100
2.2683-2.34940.19461440.145431123256100
2.3494-2.44340.22791410.154531793320100
2.4434-2.55460.19131480.153831873335100
2.5546-2.68920.18141430.144831323275100
2.6892-2.85760.17541500.157531873337100
2.8576-3.07810.20111430.162931473290100
3.0781-3.38760.17591470.15543163331099
3.3876-3.87720.20551470.146131873334100
3.8772-4.88250.1951400.134531463286100
4.8825-33.59360.18271400.16693055319596
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4718-0.1809-0.00310.45430.17181.137-0.02050.0023-0.02180.0902-0.02070.02890.02470.0014-0.00590.0869-0.0028-0.00150.0637-0.00410.090111.2255-2.831635.5243
20.2803-0.00380.08130.6832-0.14190.83890.0380.0287-0.0234-0.0077-0.07880.00820.0072-0.0167-0.03980.06630.00750.00230.11070.00850.10481.0381-6.25210.6033
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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