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- PDB-9onv: FosB from Enterococcus faecium in complex with phosphonoformate -

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Basic information

Entry
Database: PDB / ID: 9onv
TitleFosB from Enterococcus faecium in complex with phosphonoformate
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
PHOSPHONOFORMIC ACID / Metallothiol transferase FosB
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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)P30 GM124165 United States
CitationJournal: To Be Published
Title: FosB from Enterococcus faecium in complex with phosphonoformate
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)33,82012
Polymers32,8852
Non-polymers93510
Water3,351186
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 area7610 Å2
ΔGint-109 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.574, 83.574, 104.242
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-468-

HOH

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Components

#1: Protein Metallothiol transferase FosB


Mass: 16442.402 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-PPF / PHOSPHONOFORMIC ACID


Mass: 126.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 186 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, HEPES Buffer, Ammonium Sulfate, 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: DIFFRACTOMETER / Date: Feb 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→28.43 Å / Num. obs: 24283 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.1 / Redundancy: 6.3 % / Biso Wilson estimate: 31.79 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.053 / Rrim(I) all: 0.134 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.752 / Num. unique obs: 8145 / CC1/2: 0.88 / CC star: 0.968 / Rpim(I) all: 0.321 / Rrim(I) all: 0.821 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.43 Å / SU ML: 0.2524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 1932 10 %
Rwork0.1876 17387 -
obs0.1918 19319 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 60 186 2562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712421
X-RAY DIFFRACTIONf_angle_d0.9013261
X-RAY DIFFRACTIONf_chiral_restr0.054340
X-RAY DIFFRACTIONf_plane_restr0.0065409
X-RAY DIFFRACTIONf_dihedral_angle_d9.7979321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.36361330.31741196X-RAY DIFFRACTION99.85
2.26-2.320.36011350.34341210X-RAY DIFFRACTION99.04
2.32-2.380.27621360.2181223X-RAY DIFFRACTION100
2.38-2.460.25411350.21331224X-RAY DIFFRACTION100
2.46-2.550.25851350.20861214X-RAY DIFFRACTION100
2.55-2.650.25641340.22051206X-RAY DIFFRACTION100
2.65-2.770.27431380.21361242X-RAY DIFFRACTION100
2.77-2.920.30231370.20921234X-RAY DIFFRACTION100
2.92-3.10.23551370.19561235X-RAY DIFFRACTION100
3.1-3.340.23991390.18651254X-RAY DIFFRACTION100
3.34-3.670.23771380.1741241X-RAY DIFFRACTION100
3.68-4.20.17441400.14541261X-RAY DIFFRACTION100
4.21-5.290.15541430.12581282X-RAY DIFFRACTION99.93
5.29-28.430.16881520.16621365X-RAY DIFFRACTION99.74
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)
12.457959907010.172999577826-0.8161556819683.494841184020.4206354479362.50740749063-0.0563678887740.327891290329-0.294617811667-0.2385264703340.00258236439192-0.3994408659610.2943577848780.151517573273-0.01378873428210.2062436856670.02602971413310.0331817432990.244025080347-0.09657775392970.19361812442919.149-22.269-0.631
22.161672932-0.4136336322990.2082646540712.385256262510.4018622179072.13750281981-0.121917171273-0.260757390767-0.4306066438610.5047335588130.172323419338-0.09969235420760.412933070512-0.0839717878296-0.09542407038510.3648179358390.010187185324-0.01570870144160.174684114982-0.01303728596310.18561961771710.405-23.4629.025
33.29769895799-1.43332816550.3331623870581.96029262748-0.2651056352571.06839504227-0.20968184816-0.333211324688-0.282193993920.3944505851520.3045255666330.2792430186010.0973137852985-0.0860476184061-0.1103556072970.271956493642-0.009780596640890.0401257085470.180022995050.02211056911550.1274458384160.06-15.76710.213
42.35527518172-0.1314372033550.6959730313881.951424999740.1357683792022.48986905281-0.0694099569521-0.08016319015950.2006273633020.6540101626820.145087381179-0.302549947752-0.0286913653760.0518835740458-0.05507445890910.2957577650730.0137683011472-0.04572593058940.145198791939-0.06175910547620.099573670840210.488-6.08510.979
52.552871126940.143578850061-0.3914078546823.36124181225-0.04028895271423.22642072352-0.08218857876990.09348671863670.613017923293-0.2355977757520.168522319158-1.19767145468-0.2413849100540.479946080721-0.2357130798490.212837390065-0.04539687004470.05467647568520.26320276049-0.01945643412040.5766878032424.641-2.8581.271
62.93403510893-3.55960023956-1.358068775956.252188472883.422802454882.248737613280.2186482189390.2804564818540.243091612667-0.621448910980.273143973717-0.980031413648-0.1277750621610.299791910874-0.4213221217350.369735580039-0.07283305651980.1378273232230.341091299217-0.07227621146290.42074760685327.983-20.395-11.08
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:49 )A1 - 49
2X-RAY DIFFRACTION2( CHAIN A AND RESID 50:84 )A50 - 84
3X-RAY DIFFRACTION3( CHAIN A AND RESID 85:279 )A85 - 279
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:65 )B1 - 65
5X-RAY DIFFRACTION5( CHAIN B AND RESID 66:118 )B66 - 118
6X-RAY DIFFRACTION6( CHAIN B AND RESID 119:139 )B119 - 139

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