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- PDB-9ons: FosB from Enterococcus faecium in complex with methylmalonate -

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Basic information

Entry
Database: PDB / ID: 9ons
TitleFosB from Enterococcus faecium in complex with methylmalonate
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
METHYLMALONIC 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 methylmalonate
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)33,5049
Polymers32,8832
Non-polymers6217
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-138 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.468, 76.468, 115.800
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

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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, 86 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DXX / METHYLMALONIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, 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: Mar 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→27.16 Å / Num. obs: 23881 / % possible obs: 99.91 % / Redundancy: 6.7 % / Biso Wilson estimate: 43.04 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.14
Reflection shellResolution: 2.7→2.97 Å / Num. unique obs: 5856 / CC1/2: 0.143

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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→27.16 Å / SU ML: 0.3373 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.341
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 995 10.01 %
Rwork0.2182 8947 -
obs0.221 9942 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.64 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 33 79 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242389
X-RAY DIFFRACTIONf_angle_d0.47643221
X-RAY DIFFRACTIONf_chiral_restr0.0416337
X-RAY DIFFRACTIONf_plane_restr0.0028406
X-RAY DIFFRACTIONf_dihedral_angle_d16.5064873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.33411390.31231251X-RAY DIFFRACTION99.93
2.84-3.020.31941370.29351235X-RAY DIFFRACTION100
3.02-3.250.28681400.25411251X-RAY DIFFRACTION100
3.25-3.580.27081400.23871261X-RAY DIFFRACTION99.93
3.58-4.10.27251420.19991275X-RAY DIFFRACTION100
4.1-5.150.19231430.17141304X-RAY DIFFRACTION99.86
5.16-27.160.20291540.19851370X-RAY DIFFRACTION99.67
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)
15.79794120903-1.589027859860.1269495000094.631520772031.945245583794.82076348988-0.1163757076940.0956848673181-0.417616662054-0.0108763288641-0.0870472834685-0.2629801565340.4679221844250.3915304890940.1723679194270.3617552381650.04351014137280.09317215081650.2519518903620.01568459725310.33464878269521.8334404376-22.7688472553-1.15105881465
21.4447217888-1.39918341887-1.729898895493.69791728109-0.334262718213.83802850914-0.254435633162-0.145625644159-0.7534154289040.296160498984-0.05900849771780.7064354151170.384366740121-0.3157306793140.2301658987070.4334235483940.01620427481690.111078171680.3064986981990.0248465748270.5094070687546.56788381615-22.55519122445.99237015593
32.98005449776-2.018492870132.985593649816.96404977561-4.079489935223.73208983101-0.84435764912-0.933440820632-0.8541694896622.199211721340.8112711654690.7897204817170.640284702711-0.3599096604810.3863904164220.7377322150060.07867757072080.02578406052850.1723421349120.0710998032250.6560669567094.26906169492-22.652564463912.3297167715
45.3022599466-1.19814532377-1.225598621522.141385878610.3951365965971.77078572282-0.104450725256-0.1871820795070.09461862771190.3764495848970.04476243191760.4113533060160.011822470047-0.2763908109690.08053947434270.3977433302450.02155993724220.03180788556410.2240172741760.009282653910440.2966218677512.66914501741-9.907494602877.80024338009
55.12627368957-0.938552055527-0.9703621332194.081941413860.3960602072973.757899639020.114141980758-0.1884370894510.861747953870.08787024276070.106330550604-0.555526579631-0.3066731732580.0981382627965-0.2045383447030.3727638269960.0386829522146-0.01793251812630.203299696732-0.04739053411840.39314108505118.0580458337-3.919851558855.7881585043
69.038859875563.36797865192-4.622197645922.99565511973-3.303437946313.8321104828-0.820778678473-0.3529198753820.205241013518-0.978240863433-0.1669885382890.02283813869190.6516766808820.3757349021810.6931963219040.6226271247510.0666667562737-0.03805028102870.525485489568-0.06209792665140.62757638891734.3625809639-4.48096693528-1.12803976278
73.29278042205-1.56741457807-1.201527900328.901001253686.55230725676.303501923120.2406811112570.196506874280.364265853069-0.4786142292440.277533954192-1.17984866422-0.08715640897280.120255479406-0.4571154249760.35202915347-0.01762950860330.03321694767410.3137844133940.01105334661310.4778263301427.964279681-15.1768062382-6.58753468242
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 58 )AA1 - 581 - 58
22chain 'A' and (resid 59 through 85 )AA59 - 8559 - 85
33chain 'A' and (resid 86 through 97 )AA86 - 9786 - 97
44chain 'A' and (resid 98 through 139 )AA98 - 13998 - 139
55chain 'B' and (resid 1 through 85 )BD1 - 851 - 85
66chain 'B' and (resid 86 through 102 )BD86 - 10286 - 100
77chain 'B' and (resid 103 through 139 )BD103 - 139101 - 137

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