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- PDB-9oo3: N-terminal Six-His-Tagged FosB from Enterococcus faecium in compl... -

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Basic information

Entry
Database: PDB / ID: 9oo3
TitleN-terminal Six-His-Tagged FosB 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)P30 GM124165 United States
CitationJournal: To Be Published
Title: N-terminal Six-His-Tagged 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)33,2946
Polymers32,8832
Non-polymers4114
Water72140
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 area6240 Å2
ΔGint-117 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.323, 76.323, 118.125
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-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O5P / 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.: 40 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
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: Mar 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→26.98 Å / Num. obs: 24239 / % possible obs: 99.77 % / Redundancy: 7.2 % / Biso Wilson estimate: 45.36 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.79
Reflection shellResolution: 2.5→2.53 Å / Num. unique obs: 774 / CC1/2: 0.00809

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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→26.98 Å / SU ML: 0.3683 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.3295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 1262 10 %
Rwork0.2318 11353 -
obs0.2361 12615 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 18 40 2332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282343
X-RAY DIFFRACTIONf_angle_d0.50963167
X-RAY DIFFRACTIONf_chiral_restr0.0441334
X-RAY DIFFRACTIONf_plane_restr0.0046399
X-RAY DIFFRACTIONf_dihedral_angle_d16.8234853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.37041360.32251220X-RAY DIFFRACTION100
2.6-2.720.35391380.30441245X-RAY DIFFRACTION100
2.72-2.860.35191370.30891234X-RAY DIFFRACTION100
2.86-3.040.39171370.32771238X-RAY DIFFRACTION100
3.04-3.270.31231400.26631262X-RAY DIFFRACTION99.93
3.28-3.60.28271390.24861248X-RAY DIFFRACTION99.93
3.6-4.120.25031410.2161259X-RAY DIFFRACTION100
4.12-5.190.21961430.16411293X-RAY DIFFRACTION99.86
5.19-26.980.2411510.19831354X-RAY DIFFRACTION98.37
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)
11.6697745352-0.763540976112-0.495894778842.397724366850.7976772796571.47082114917-0.274607142560.293236913218-0.4854226151990.6435989345590.02013319306220.1214828281220.3895563555160.0554665527197-0.02473956951310.4401854440140.04754159946510.05884087071920.21933820831-0.03566937201560.33908266270217.0959438285-22.21263725160.966691922398
21.29098505212-0.7577323126321.0137093522.29244796431-0.6606467753290.812907940875-0.354956679823-0.432217280326-0.33471172310.7870182143390.09051475930590.310515008880.616980252561-0.332238561432-0.1768798033120.742082564214-0.05263578900830.3117965451940.1868340656040.05774377798880.4710029013342.47052738573-21.203637973210.3127799126
30.5698143677020.3494474698290.07994122229880.3005469112690.1101098649640.684328844817-0.0971187287015-0.0185835601147-0.07626994509050.497074161415-0.1853516352880.3134076752080.329543748082-0.2277216824580.000107542287220.541462309875-0.02020297147410.07014721413720.364554298415-0.01951074458170.3506278390713.68223340098-8.63056416047.73744557926
41.43829600843-1.035078512250.3310333737671.572176566220.3940700752351.27120150493-0.0876951326418-0.05890599768410.4424614478710.3913548800490.0682320723208-0.3416961155940.0575210258138-0.0385982114687-0.0005986183987980.3914091144670.0402648394521-0.01523133255150.260323145739-0.0005779532592470.34007715227517.5698560635-3.998370663795.65540472603
50.2327951773030.0505272481586-0.1071981453340.0426260919813-0.01701506121650.0441489876037-0.3343473975830.3312695002110.418708261770.168109036433-0.0543480156709-0.269337593315-0.132015619020.833395307319-0.0006477403944350.4801746637080.0527980516215-0.1668329265550.6093408328070.06533762441710.77122955392432.1259515281-2.195187403370.623621551569
60.2147006708090.01600238455030.07621594033280.237168292348-0.05036178783690.2487404997850.1186015130850.09019292460470.114355196390.3390615529930.247291039232-0.6035801952880.223885870734-0.2720292840820.004247425835230.4492745877010.0692505400102-0.07869920443280.404567794106-0.02892575170550.45050061464925.6742488393-7.42372427327-0.595998086224
70.0887487896537-0.0882531513696-0.04511533740410.1776778765010.131434646310.08838149471430.2562501538320.196251206289-0.226021533719-0.309766633245-0.190697711475-0.521155407574-0.222800536293-0.1733383471310.0008671881532110.4807009440830.02879849591680.01586516922250.480891014437-0.1464903891170.54964446358630.3981762669-22.4175415545-14.3920976778
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 83 )AA1 - 831 - 83
22chain 'A' and (resid 84 through 105 )AA84 - 10584 - 105
33chain 'A' and (resid 106 through 139 )AA106 - 139106 - 139
44chain 'B' and (resid 1 through 83 )BC1 - 831 - 83
55chain 'B' and (resid 84 through 101 )BC84 - 10184 - 95
66chain 'B' and (resid 102 through 122 )BC102 - 12296 - 116
77chain 'B' and (resid 123 through 139 )BC123 - 139117 - 133

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