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- PDB-4jh4: Crystal Structure of FosB from Bacillus cereus with Nickel and Fo... -

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Basic information

Entry
Database: PDB / ID: 4jh4
TitleCrystal Structure of FosB from Bacillus cereus with Nickel and Fosfomycin
ComponentsMetallothiol transferase FosB
KeywordsTRANSFERASE / Bacillithiol-S-Transferase
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (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 / NICKEL (II) ION / Metallothiol transferase FosB
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)33,3706
Polymers32,9772
Non-polymers3944
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-62 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.405, 68.540, 70.443
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: fosB, BCE_2111 / Production host: Escherichia coli (E. coli)
References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
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: 1.48 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: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25076 / % possible obs: 98.4 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.126 / Χ2: 1.759 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9314.10.79212071.041197
1.93-1.9714.10.70712191.1196.8
1.97-2.0114.30.59511951.154196.8
2.01-2.0514.30.48612211.203197.5
2.05-2.0914.40.41412221.286196.9
2.09-2.1414.50.37512371.263197.6
2.14-2.1914.40.30812181.362198.4
2.19-2.2514.50.2912201.385197.5
2.25-2.3214.50.25212281.479197.6
2.32-2.3914.50.21812611.401198.1
2.39-2.4814.50.20312331.438198.8
2.48-2.5814.50.18412571.5198.7
2.58-2.714.50.14812411.656198.6
2.7-2.8414.50.12412661.784199.3
2.84-3.0214.40.09712631.913199.4
3.02-3.2514.40.07512832.174199.3
3.25-3.5814.10.06612882.517199.8
3.58-4.0913.80.05712952.821199.7
4.09-5.1613.80.04913133.077199.9
5.16-5012.90.05314093.468199.5

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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: 1.9→49.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2065 / WRfactor Rwork: 0.1664 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8748 / SU B: 2.655 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1414 / SU Rfree: 0.1354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 1266 5.1 %RANDOM
Rwork0.1722 ---
obs0.1745 25035 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.39 Å2 / Biso mean: 19.2823 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0 Å2
2---0.08 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 18 142 2484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022396
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9473236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.15723.944142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32715416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.241518
X-RAY DIFFRACTIONr_chiral_restr0.1570.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021864
LS refinement shellResolution: 1.893→1.942 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 89 -
Rwork0.18 1518 -
all-1607 -
obs--94.81 %

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