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- PDB-9onl: FosB from Enterococcus faecium in complex with phosphonoacetate -

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Basic information

Entry
Database: PDB / ID: 9onl
TitleFosB from Enterococcus faecium in complex with phosphonoacetate
ComponentsMetallothiol transferase FosB
KeywordsHYDROLASE / Inhibitor / metalloenzyme / antibiotic resistance
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / response to antibiotic / metal ion binding
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
PHOSPHONOACETIC ACID / Metallothiol transferase FosB
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBenton, H.M. / Thompson, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165 United States
CitationJournal: To Be Published
Title: FosB from Enterococcus faecium in complex with phosphonoacetate
Authors: Benton, H.B. / Thompson, M.K.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,5749
Polymers32,8832
Non-polymers6917
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The assembly is defined by the asymmetric unit observed in the crystal structure and supported by the coordination of inhibitors at the active site.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-131 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.789, 83.789, 103.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-369-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, magnesium chloride, ammonium sulfate

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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: DIFFRACTOMETER / Date: Mar 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→26.97 Å / Num. obs: 25547 / % possible obs: 99.78 % / Redundancy: 5.4 % / CC1/2: 0.973 / CC star: 0.993 / Net I/σ(I): 6.62
Reflection shellResolution: 2.5→2.75 Å / Num. unique obs: 6234 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.97 Å / SU ML: 0.3556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 1331 10 %
Rwork0.2256 11973 -
obs0.2286 13304 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 35 139 2442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342351
X-RAY DIFFRACTIONf_angle_d0.65243176
X-RAY DIFFRACTIONf_chiral_restr0.0453334
X-RAY DIFFRACTIONf_plane_restr0.0055398
X-RAY DIFFRACTIONf_dihedral_angle_d7.6149307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.37081300.30951172X-RAY DIFFRACTION100
2.59-2.690.35161300.29191168X-RAY DIFFRACTION100
2.69-2.820.33281310.30031177X-RAY DIFFRACTION100
2.82-2.960.32121310.29781183X-RAY DIFFRACTION100
2.96-3.150.29491300.251175X-RAY DIFFRACTION99.92
3.15-3.390.28551320.2351184X-RAY DIFFRACTION99.92
3.39-3.730.23441340.21081199X-RAY DIFFRACTION100
3.73-4.270.22231330.18251200X-RAY DIFFRACTION99.78
4.27-5.370.17581370.16651230X-RAY DIFFRACTION100
5.37-26.970.22311430.211285X-RAY DIFFRACTION98.28
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)
13.34856272447-0.344060740923-0.6358452270224.68642259788-0.668016651752.348738665-0.1173184730260.148552762785-0.3516876715270.1185620645080.137033152615-0.3686817028260.3458164644880.130470576834-0.01323036986810.271405050010.048049359349-0.0231447921740.170386668731-0.06513057891340.14426420231615.0035093354-23.2020238413.64713433343
22.56122193878-1.680934335790.6612780578453.74440690810.548768593760.946977225929-0.217967962-0.427972307135-0.1105777846650.4364013017320.2038637388090.2498472493690.0119384972775-0.0295332972464-0.121553415040.259664750013-0.02002071769820.05529388544220.2560901752490.04110643152540.182087088102-0.295131335695-14.723132729910.1962817562
33.97095803301-1.782086021630.5585548966884.78632752141-0.8836400071223.08057747526-0.000627382133868-0.03708031184530.4500414903390.5296926484140.0529541124563-0.931211267732-0.2439326854990.188629447846-0.03331792189340.254522089531-0.0463942882354-0.07108726818290.112303715027-0.04580796435630.2403516731814.6572711143-3.886466216617.7315477004
44.935180377440.9743956110292.252690568593.24487228817-1.918279561225.7769079089-0.1687972103040.1333077359270.135917723055-0.203002402089-0.153655762664-0.7575404992940.1935279110040.579622206531-0.1334727753780.212258925474-0.00479383484678-0.04390991948950.204853023416-0.05154853910670.49519472268423.0105027049-5.953921244344.51140797864
53.04780977071-4.95767764319-1.5253475987.981392164522.887953364471.276664274590.01210296918930.2093587488770.4811910541210.131363268636-0.0151172842134-1.051644637990.3272489649450.20988411907-0.07395137193350.445894538125-0.02561958715640.1091888023950.322999675099-0.02121639744440.57138331493527.7141129753-19.3082657715-10.6060347976
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 86 )AA1 - 861 - 86
22chain 'A' and (resid 87 through 139 )AA87 - 13987 - 139
33chain 'B' and (resid 1 through 99 )BD1 - 991 - 94
44chain 'B' and (resid 100 through 116 )BD100 - 11695 - 111
55chain 'B' and (resid 117 through 139 )BD117 - 139112 - 134

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