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- PDB-7n7g: Crystal Structure of FosB from Enterococcus faecium with Fosfomycin -

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Basic information

Entry
Database: PDB / ID: 7n7g
TitleCrystal Structure of FosB from Enterococcus faecium with Fosfomycin
ComponentsMetallothiol transferase FosB
KeywordsTRANSFERASE/ANTIBIOTIC / fosfomycin / antibiotic resistance / thiol-transferase / ANTIBIOTIC / dimer / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / response to antibiotic / metal 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
FOSFOMYCIN / : / Metallothiol transferase FosB
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsShay, M.R. / Simmons, Z. / Thompson, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Cystic Fibrosis FoundationTHOMPS20I0 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Structural and functional characterization of fosfomycin resistance conferred by FosB from Enterococcus faecium.
Authors: Wiltsie, V. / Travis, S. / Shay, M.R. / Simmons, Z. / Frantom, P. / Thompson, M.K.
History
DepositionJun 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,64112
Polymers32,8832
Non-polymers75810
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-26 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.874, 79.874, 95.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Metallothiol transferase FosB


Mass: 16441.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: fosB / Production host: Escherichia coli (E. coli) / References: UniProt: F1C939
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID


Mass: 138.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H7O4P / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mg/mL protein in 20mM HEPES pH7.5, 38% PEG MME 550, 150mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→23.8 Å / Num. obs: 21556 / % possible obs: 99.7 % / Redundancy: 18.1 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 1.74
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.745 / Num. unique obs: 2159

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
SCALAdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JH2

4jh2


Resolution: 2→23.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.343 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1078 5 %RANDOM
Rwork0.2135 ---
obs0.2156 20380 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.84 Å2 / Biso mean: 31.256 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.87 Å2
Refinement stepCycle: final / Resolution: 2→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 62 96 2386
Biso mean--44.94 39.86 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172030
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.6433084
X-RAY DIFFRACTIONr_angle_other_deg1.331.5794687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8135268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28623.223121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.412159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 78 -
Rwork0.275 1470 -
all-1548 -
obs--99.94 %

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