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- PDB-9onp: FosB from Enterococcus faecium in complex with (1-Hydroxy-2-methy... -

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Basic information

Entry
Database: PDB / ID: 9onp
TitleFosB from Enterococcus faecium in complex with (1-Hydroxy-2-methylpropyl)phosphonic acid
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
[(1R)-1-hydroxy-2-methylpropyl]phosphonic acid / Metallothiol transferase FosB
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 (1-Hydroxy-2-methylpropyl)phosphonic acid
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)33,4147
Polymers32,8832
Non-polymers5315
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-118 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.438, 77.438, 120.100
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

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-YS8 / [(1R)-1-hydroxy-2-methylpropyl]phosphonic acid


Mass: 154.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O4P / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.07 %
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 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→27.38 Å / Num. obs: 23881 / % possible obs: 98.03 % / Redundancy: 6.7 % / Biso Wilson estimate: 65.06 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.14
Reflection shellResolution: 2.5→2.53 Å / Num. unique obs: 363 / CC1/2: 0.115

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→27.38 Å / SU ML: 0.4749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2925 1055 10 %
Rwork0.2538 9496 -
obs0.2576 10551 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.16 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 26 23 2295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272322
X-RAY DIFFRACTIONf_angle_d0.55373140
X-RAY DIFFRACTIONf_chiral_restr0.0441333
X-RAY DIFFRACTIONf_plane_restr0.0026392
X-RAY DIFFRACTIONf_dihedral_angle_d17.9685841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.43241260.40221141X-RAY DIFFRACTION99.92
2.82-2.970.38731310.34931178X-RAY DIFFRACTION100
2.97-3.160.38131280.34681144X-RAY DIFFRACTION100
3.16-3.40.32451310.31171187X-RAY DIFFRACTION100
3.4-3.740.33671290.26821157X-RAY DIFFRACTION100
3.74-4.280.2871330.23821196X-RAY DIFFRACTION99.85
4.28-5.390.23261340.19941202X-RAY DIFFRACTION100
5.39-27.380.25281430.2181291X-RAY DIFFRACTION99.65
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)
16.34588978413-2.026819051-2.547740546756.089540420321.750426263275.88791640557-0.911546915388-0.0829653604519-1.280812531881.095552537240.5038276818420.2301868992251.02702279910.1938698826310.2018358693060.7092560401910.1044081245550.1012234583570.3709256090040.001044956256440.53985127487815.2183027994-23.17745696472.3865678634
27.44427596339-3.6917817946-1.777096663715.897043748222.065348027913.03892344521-0.698606066899-0.554691454818-0.1494048205490.9175514545490.1762564848810.7919603332990.479831141287-0.06861068818990.431405635690.5989475332680.01850537230480.07860070725320.4062185954780.06063354602760.4018961005162.06450962624-10.74553993218.02299893323
37.33906668222-2.34148206988-1.074307592394.109489702780.5663683911362.81073052891-0.463700727121-1.079957823111.406059640091.182877097180.811731216108-0.8166403799680.2473229288670.345267095925-0.2516938919330.6887683438170.107852414434-0.1674696067970.541597374785-0.1989659576810.61236935917312.8870843145-4.741160980778.86288645431
44.15006470389-0.368165959737-0.119767336583.872677737612.795869640392.057912183230.1505863203880.2937869558952.19513544197-0.562013866720.271694845882-2.74704521346-0.8941662185390.92724933738-0.2379503272010.5540073583690.004756705586590.1442126590080.551688058674-0.1572587209741.9492743558826.6712077248-3.14182113154-1.16852119751
51.94911045935-2.243483861671.410692197196.51544939927-1.371640129335.26399967314-0.302997090878-0.6052528388782.467590290610.005211486907110.0205783413408-3.050470201210.3711793546540.860423363332-1.254609782640.347836127730.0402305591699-0.3007627307370.805687464072-0.5652424844021.5206416146727.384036732-5.048097970692.84151936473
64.48753970815-3.7391387353-3.24789274933.556989119923.753563691638.277946376290.7644632845090.2200731726530.9779146447070.163851937299-0.541462545855-1.3456427857-0.4864841345420.464874976893-0.5564964461670.5856244176090.01196637006340.1135684075720.799931468252-0.04686457155890.77509402554629.0883806975-21.7340172007-14.4483353775
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 96 )AA1 - 961 - 96
22chain 'A' and (resid 97 through 139 )AA97 - 13997 - 139
33chain 'B' and (resid 1 through 59 )BD1 - 591 - 59
44chain 'B' and (resid 60 through 85 )BD60 - 8560 - 85
55chain 'B' and (resid 86 through 119 )BD86 - 11986 - 110
66chain 'B' and (resid 120 through 139 )BD120 - 139111 - 130

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