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- PDB-4jh5: Crystal Structure of FosB from Bacillus cereus with Cobalt and Fo... -

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Basic information

Entry
Database: PDB / ID: 4jh5
TitleCrystal Structure of FosB from Bacillus cereus with Cobalt 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 / SAD / Resolution: 1.77 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 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Feb 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_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.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.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

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Assembly

Deposited unit
A: Metallothiol transferase FosB
B: Metallothiol transferase FosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4208
Polymers32,9772
Non-polymers4436
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-74 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.327, 68.230, 69.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: BCE_2111, fosB / Production host: Escherichia coli (E. coli)
References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
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: 1.6046 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6046 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 30425 / % possible obs: 98.8 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.095 / Χ2: 3.922 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.8130.39814451.132195.6
1.8-1.8314.10.32214691.287197.1
1.83-1.8714.10.27314791.468198.1
1.87-1.9114.10.23914741.705197.3
1.91-1.9514.10.20114892.1197.8
1.95-1.99140.17714922.338198.5
1.99-2.04140.15914902.789198.5
2.04-2.113.90.1514953.131198.2
2.1-2.1613.70.13815113.544198.6
2.16-2.2313.60.1315053.797198.8
2.23-2.3113.70.12115144.03199.1
2.31-2.413.70.11315174.176199.4
2.4-2.5113.70.11315274.352199.4
2.51-2.6413.50.10515294.796199.7
2.64-2.81130.10315455.702199.7
2.81-3.03130.0915445.935199.9
3.03-3.3312.50.07715586.3161100
3.33-3.8112.10.07215686.6051100
3.81-4.812.10.06715826.7441100
4.8-5011.30.07116927.419199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→48.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.1766 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8794 / SU B: 1.958 / SU ML: 0.064 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.1123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1530 5 %RANDOM
Rwork0.1694 ---
obs0.1715 30378 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.7 Å2 / Biso mean: 17.3269 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0 Å2
2---0.37 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 20 184 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022417
X-RAY DIFFRACTIONr_angle_refined_deg2.2041.9463270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.90823.958144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4381518
X-RAY DIFFRACTIONr_chiral_restr0.1810.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021887
LS refinement shellResolution: 1.767→1.813 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 95 -
Rwork0.227 1859 -
all-1954 -
obs--93.85 %

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