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- PDB-8g7i: Crystal Structure of FosB from Bacillus cereus with Zinc and Sulfate -

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Basic information

Entry
Database: PDB / ID: 8g7i
TitleCrystal Structure of FosB from Bacillus cereus with Zinc and Sulfate
ComponentsMetallothiol transferase FosB
KeywordsTRANSFERASE / FosB / inhibitor / homodimer / bacillithiol-S-transferase
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / response to antibiotic / magnesium ion binding / cytoplasm
Similarity search - Function
Metallothiol transferase FosB / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
FORMIC ACID / Metallothiol transferase FosB
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsTravis, S. / Pang, A.H. / Tsodikov, O.V. / Garneau-Tsodikova, S. / Thompson, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM148956 United States
CitationJournal: Rsc Med Chem / Year: 2023
Title: Identification and analysis of small molecule inhibitors of FosB from Staphylococcus aureus.
Authors: Travis, S. / Green, K.D. / Thamban Chandrika, N. / Pang, A.H. / Frantom, P.A. / Tsodikov, O.V. / Garneau-Tsodikova, S. / Thompson, M.K.
History
DepositionFeb 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallothiol transferase FosB
B: Metallothiol transferase FosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,67114
Polymers32,9772
Non-polymers69412
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-168 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.494, 68.402, 70.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallothiol transferase FosB / Fosfomycin resistance protein


Mass: 16488.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: fosB, BCE_2111 / Production host: Escherichia coli (E. coli)
References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Non-polymers , 6 types, 270 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM methylmalonate) and reservoir solution (50 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX ...Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM methylmalonate) and reservoir solution (50 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate with a 2:3 ratio of protein:reservoir solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 27845 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.988 / Χ2: 0.062 / Net I/σ(I): 4.3 / Num. measured all: 296039
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.83-1.865.40.75326610.424199.8
1.86-1.95.50.66726400.434199.9
1.9-1.935.40.5725970.466199.7
1.93-1.975.10.46526420.485199.8
1.97-2.015.10.40626370.51199.9
2.01-2.0660.37226440.502199.8
2.06-2.1160.33326230.528199.8
2.11-2.1760.28226460.5381100
2.17-2.2360.24126360.5571100
2.23-2.315.90.21726450.571100
2.31-2.395.80.18926290.61100
2.39-2.485.80.17926570.586199.9
2.48-2.65.60.15926280.613199.7
2.6-2.735.30.13226390.639199.7
2.73-2.94.90.10626180.695199.2
2.9-3.135.90.09326180.776199.7
3.13-3.4460.07426490.854199.8
3.44-3.945.90.05926440.958199.9
3.94-4.975.20.05426391.04199.8
4.97-505.30.0626161.063198.6

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Processing

Software
NameVersionClassification
REFMAC8.0.008refinement
SCALEPACK8.0.007data scaling
PHASER8.0.004phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→48.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18797 1456 5.2 %RANDOM
Rwork0.15923 ---
obs0.1607 26425 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.83→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 35 258 2617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132459
X-RAY DIFFRACTIONr_bond_other_d0.0350.0152205
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.6383312
X-RAY DIFFRACTIONr_angle_other_deg2.2741.5845074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65622.303165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96715424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1881519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022822
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02624
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4321.6091126
X-RAY DIFFRACTIONr_mcbond_other1.4311.6121127
X-RAY DIFFRACTIONr_mcangle_it2.0162.4051413
X-RAY DIFFRACTIONr_mcangle_other2.0152.4061414
X-RAY DIFFRACTIONr_scbond_it2.4961.9791333
X-RAY DIFFRACTIONr_scbond_other2.4821.9691316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8842.8281888
X-RAY DIFFRACTIONr_long_range_B_refined5.57720.1172825
X-RAY DIFFRACTIONr_long_range_B_other5.58120.0972823
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.864 Å
RfactorNum. reflection% reflection
Rfree0.244 115 -
Rwork0.238 1753 -
obs--91.21 %

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