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- PDB-9onw: N-terminal Six-His-Tagged FosB from Enterococcus faecium in compl... -

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Basic information

Entry
Database: PDB / ID: 9onw
TitleN-terminal Six-His-Tagged FosB 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: 2.8 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: N-terminal Six-His-Tagged FosB from Enterococcus faecium in complex with fosfomycin
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)33,3226
Polymers32,8832
Non-polymers4394
Water1629
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 area5920 Å2
ΔGint-115 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.211, 76.211, 119.138
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-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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 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: Apr 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→27.74 Å / Num. obs: 24224 / % possible obs: 94.31 % / Redundancy: 5.2 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.837 / Net I/σ(I): 1.46
Reflection shellResolution: 2.7→2.73 Å / Num. unique obs: 765 / CC1/2: 0.116

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→27.74 Å / SU ML: 0.5735 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3246 889 10.01 %
Rwork0.2919 7993 -
obs0.2952 8882 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.76 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 20 9 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292379
X-RAY DIFFRACTIONf_angle_d0.5033217
X-RAY DIFFRACTIONf_chiral_restr0.0431340
X-RAY DIFFRACTIONf_plane_restr0.0081405
X-RAY DIFFRACTIONf_dihedral_angle_d5.5115310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.55551330.54131197X-RAY DIFFRACTION89.32
2.98-3.20.38761470.37371325X-RAY DIFFRACTION99.53
3.2-3.530.40031490.35291336X-RAY DIFFRACTION99
3.53-4.040.34241500.28361353X-RAY DIFFRACTION99.21
4.04-5.080.25131510.23011361X-RAY DIFFRACTION98.82
5.08-27.740.26451590.24461421X-RAY DIFFRACTION96.81
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)
12.69187045424-1.476643654981.735627184195.35255046566-3.091246768614.10172493453-0.2774591056850.186604039885-0.07604532128440.5140226164230.1476715406430.3707132040170.3826608216880.3375784603890.2145795401240.5333399863840.07143070004280.04689732627190.486800515201-0.1703622658930.13156367827421.0943191917-13.6650755406-1.5820541266
21.595037218770.511643998182-1.421105154661.20852097108-1.119835699921.6669721623-0.161099208490.0877606189926-0.6824591130360.134393551472-0.211655172422-0.11633832981.18966027863-0.2011914754310.3413227526081.398398759930.1142392884430.342924922420.144981883229-0.1846290842250.86533836084119.0878196057-30.3667361271-0.20474240541
34.990379659110.68626471828-0.1338285392891.00710526215-0.5509962926172.2028690855-0.5397132684270.16647904587-1.23533052710.6125746940430.4394484691780.2824737595140.3121626902750.2527325123150.07883096216770.5683150318090.08124227120190.161742295690.389514721646-0.1482788114770.58808231461923.2865712279-23.5168733019-1.6858168763
42.238362099552.521608165111.154265682154.037287734323.237608398293.77260775741-0.062123893989-0.438314502068-0.7241844900441.481746543250.2856061123540.2124898813140.704061659103-0.2854794078840.006152432607531.06068215540.1673994177270.1627403697350.456811153063-0.0441412206110.50612716146217.4707452635-16.449542687816.495349651
54.60261442642-0.6033397532512.359238379472.057794917511.429289824112.743147904870.473544989588-0.00330732205421-0.5434376010870.297280723734-0.1374876122870.5503846603880.801014578185-0.431745352958-0.1657344025340.700861256747-0.1141805009050.2675101209670.5051601089950.1010114095780.4678042759213.9914059524-18.97936271470.69039029456
67.81494013624-1.39576498005-0.763820450140.3876032925311.173576278257.50893596396-0.419900232215-0.710216499905-1.297442714080.5117563948860.4486350711990.52417469231.076089893890.0531524250580.4700010350090.84635711498-0.0768853587350.4876376331390.45555707284-0.1079382800690.9982436677032.53016479737-29.99547939144.02701967935
71.38186446191-0.5793061583070.5356850667720.211170753755-0.2281260775040.869406706542-0.521217643897-0.791494083956-0.293180889391-0.1452818531050.505768455369-0.07171390902350.557974313010.0942326188567-0.07919627717941.3267099919-0.0748855617360.5193291249280.548060982412-0.02527003163720.3452622434015.02545398908-23.082111470312.425498772
81.504796043610.3611016326010.2502849886090.8406680612771.09112491223.470267775130.340826865566-0.255782219969-0.431342555510.224690528051-0.0169081961971-0.2379554021031.18823752495-0.12351477752-0.2499168924340.958821772868-0.1147165785410.2048528383470.4610835522810.03948174571040.4815611222951.12232827164-17.4924641748.4885876447
90.5067728474320.438653015134-0.2284500373551.09395233224-0.8330492464540.741910152672-0.0713182863196-0.13448417867-0.560394234401-0.0141886135797-0.6080835007620.1160230264450.2947076819090.322616704225-0.1278394920180.9365605857140.1294498398630.0340423647568-0.0925506108672-0.2425111619030.69159422081710.2909914122-18.6551069415.7839479486
107.50044429704-2.82439423815-2.860775063687.947280413093.107855744882.059044709440.1224280772280.202691107578-0.4154247904680.564508634515-0.2804354322791.191488738520.103152302199-0.1529882506430.5165578305760.4571463770560.06377627419170.05705331867070.3835445295990.0997028060040.647789511732-3.72181396402-4.262149889327.12542163137
117.27237143038-0.1838734873694.341793451438.32127284843-1.200461959255.361365941030.529890128549-0.09119921617740.6244525244881.50209719947-1.087792612840.9416956019420.734145059756-0.4744363817630.6162065860480.992562085976-0.01504421567680.2021465665070.458226574879-0.05104721351610.4071054580630.0945359081613.3209744199711.2566004641
122.99797944019-1.184206810740.3199079232242.112527700370.4719933858971.00624668964-0.202747582994-0.2194043366160.1371197292740.2965375643780.0986848568682-0.2272028669120.2846776043240.2099423551770.104139165930.555396223770.0631278987976-0.007673183859090.354884448765-0.05363164673990.2525310049614.5387223086-5.387004044518.92041762374
134.1245393796-1.59170490601-2.350336490371.106291587620.7856491967892.370013370980.1259544106350.4756466462560.127062632166-0.204316991912-0.179611907434-1.04299592221-0.160920363020.3435142454920.08101120705160.4876021657250.0488404845770.004113993722460.462185707574-0.06651856384520.6765696675529.3628848134-2.35267152328-3.38059882564
144.2001195466-0.6498609618870.2981934466253.501913327231.693417867681.30416722458-0.1498519223170.07910708085960.186843574846-0.4298873910020.433359046341-0.908834134353-0.2926874378120.51576947955-0.2008986002070.4655026181520.0828097445078-0.06122974613350.394513483045-0.0817206613130.27424456124227.5129938879-14.6851124522-7.13318384253
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 14 )AA1 - 141 - 14
22chain 'A' and (resid 15 through 24 )AA15 - 2415 - 24
33chain 'A' and (resid 25 through 58 )AA25 - 5825 - 58
44chain 'A' and (resid 59 through 65 )AA59 - 6559 - 65
55chain 'A' and (resid 66 through 75 )AA66 - 7566 - 75
66chain 'A' and (resid 76 through 85 )AA76 - 8576 - 85
77chain 'A' and (resid 86 through 97 )AA86 - 9786 - 97
88chain 'A' and (resid 98 through 107 )AA98 - 10798 - 107
99chain 'A' and (resid 108 through 121 )AA108 - 121108 - 121
1010chain 'A' and (resid 122 through 131 )AA122 - 131122 - 131
1111chain 'A' and (resid 132 through 139 )AA132 - 139132 - 139
1212chain 'B' and (resid 1 through 65 )BC1 - 651 - 65
1313chain 'B' and (resid 66 through 102 )BC66 - 10266 - 101
1414chain 'B' and (resid 103 through 139 )BC103 - 139102 - 138

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