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- PDB-4jh6: Crystal Structure of FosB from Bacillus cereus with Manganese and... -

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Basic information

Entry
Database: PDB / ID: 4jh6
TitleCrystal Structure of FosB from Bacillus cereus with Manganese and Fosfomycin
ComponentsMetallothiol transferase FosB
KeywordsTRANSFERASE / Bacillithiol-S-Transferase
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / response to antibiotic / magnesium ion binding / cytoplasm
Similarity search - Function
Metallothiol transferase FosB / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
FOSFOMYCIN / : / Metallothiol transferase FosB
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsThompson, M.K. / Harp, J. / Keithly, M.E. / Jagessar, K. / Cook, P.D. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Chemical Aspects of Resistance to the Antibiotic Fosfomycin Conferred by FosB from Bacillus cereus.
Authors: Thompson, M.K. / Keithly, M.E. / Harp, J. / Cook, P.D. / Jagessar, K.L. / Sulikowski, G.A. / Armstrong, R.N.
History
DepositionMar 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,64412
Polymers32,9772
Non-polymers66710
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-76 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.488, 68.691, 70.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallothiol transferase FosB / Fosfomycin resistance protein


Mass: 16488.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: fosB, BCE_2111 / Production host: Escherichia coli (E. coli)
References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID


Mass: 138.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O4P / Comment: antibiotic*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, Magnesium formate, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.13 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 72030 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.051 / Χ2: 1.538 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.32-1.343.70.54836560.731199.9
1.34-1.373.90.48636030.7261100
1.37-1.393.90.43736170.7761100
1.39-1.423.90.38136380.7881100
1.42-1.453.90.3136470.808199.9
1.45-1.493.90.26136500.842199.9
1.49-1.5240.22636290.899199.6
1.52-1.5740.18436251.033199.7
1.57-1.6140.16736281.261199.5
1.61-1.6640.14736191.421199.2
1.66-1.724.10.12936431.415199.1
1.72-1.794.10.10636141.42198.7
1.79-1.874.10.08236091.421198.6
1.87-1.974.10.07236051.765198
1.97-2.14.10.06935972.533197.5
2.1-2.264.20.0635832.593196.7
2.26-2.484.20.04935782.318196.2
2.48-2.844.30.04335272.424194.9
2.84-3.584.30.03535082.486192.7
3.58-504.20.03234542.652187.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→49.06 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1752 / WRfactor Rwork: 0.1412 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9101 / SU B: 1.48 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0462 / SU Rfree: 0.0459 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 3622 5 %RANDOM
Rwork0.1379 ---
obs0.1395 71982 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.21 Å2 / Biso mean: 20.376 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0 Å2
2---0.22 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.32→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 34 247 2605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192510
X-RAY DIFFRACTIONr_angle_refined_deg2.2041.953401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.19923.741147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65115438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6621521
X-RAY DIFFRACTIONr_chiral_restr0.1690.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021971
X-RAY DIFFRACTIONr_rigid_bond_restr8.08632510
X-RAY DIFFRACTIONr_sphericity_free18.714557
X-RAY DIFFRACTIONr_sphericity_bonded13.90452645
LS refinement shellResolution: 1.32→1.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 255 -
Rwork0.219 4674 -
all-4929 -
obs--97.53 %

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