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- PDB-5u7b: Crystal structure of a the tin-bound form of MerB formed from Die... -

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Basic information

Entry
Database: PDB / ID: 5u7b
TitleCrystal structure of a the tin-bound form of MerB formed from Diethyltin.
ComponentsAlkylmercury lyase
KeywordsLYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / Mercury / Diethyltin
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 / Diethyltin dichloride / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 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 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

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Assembly

Deposited unit
A: Alkylmercury lyase
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8107
Polymers46,1172
Non-polymers6935
Water2,720151
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4454
Polymers23,0581
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3653
Polymers23,0581
Non-polymers3072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.860, 88.802, 55.010
Angle α, β, γ (deg.)90.000, 97.190, 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-BR / BROMIDE ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN6 / Diethyltin dichloride


Mass: 247.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10Cl2Sn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 38.17 %
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 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22423 / % possible obs: 92 % / Redundancy: 2.7 % / Net I/σ(I): 12.07

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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: 5U79

5u79


Resolution: 2→46.497 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.224 3734 8.96 %
Rwork0.1654 --
obs0.1707 22423 86.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.11 Å2 / Biso mean: 46.5511 Å2 / Biso min: 18.3 Å2
Refinement stepCycle: final / Resolution: 2→46.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 17 151 3346
Biso mean--26.17 41.31 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133254
X-RAY DIFFRACTIONf_angle_d1.3834437
X-RAY DIFFRACTIONf_chiral_restr0.055525
X-RAY DIFFRACTIONf_plane_restr0.008571
X-RAY DIFFRACTIONf_dihedral_angle_d14.2221161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.02540.3415750.282478786249
2.0254-2.05210.3254840.241289397756
2.0521-2.08020.3167960.2382992108860
2.0802-2.10990.2421060.23961038114463
2.1099-2.14140.26461160.21241169128573
2.1414-2.17480.22281240.20371242136679
2.1748-2.21050.23391450.21391465161090
2.2105-2.24860.27341500.18491525167594
2.2486-2.28950.23451530.19371518167194
2.2895-2.33350.23411490.18911497164693
2.3335-2.38120.24871520.19221552170494
2.3812-2.43290.25261470.191484163193
2.4329-2.48950.22511510.18361529168094
2.4895-2.55180.28521510.18371529168095
2.5518-2.62080.25791530.17051536168994
2.6208-2.69790.24751480.17091524167294
2.6979-2.7850.26041450.17871508165395
2.785-2.88450.27651520.1881524167693
2.8845-30.28151480.18661521166994
3-3.13650.23621490.1841513166292
3.1365-3.30180.24731410.18591517165895
3.3018-3.50860.23781490.17921523167293
3.5086-3.77940.25281500.16041502165293
3.7794-4.15950.17411540.14061529168393
4.1595-4.76080.15721430.12761492163593
4.7608-5.99620.20881510.13141508165994
5.9962-46.510.16311520.12571505165793
Refinement TLS params.

S33: 0.0001 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.912-0.3893-0.22230.70310.01830.9901-0.01760.0102-0.0396-0.0498-0.08060.14220.0583-0.00790.2587-0.01240.01070.2256-0.02560.235911.4204-4.791535.9187
20.8697-0.52790.29461.6665-0.25081.31510.01830.0969-0.0860.0819-0.03850.10140.0297-0.00520.1653-0.01510.0010.26450.03170.24820.9892-8.307311.0324
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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