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- PDB-4jh9: Crystal Structure of FosB from Bacillus cereus with Maganese and ... -

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Basic information

Entry
Database: PDB / ID: 4jh9
TitleCrystal Structure of FosB from Bacillus cereus with Maganese and Potential BSH-Fosfomycin Product
ComponentsMetallothiol transferase FosB
Keywordstransferase/transferase inhibitor / Bacillithiol-S-Transferase / transferase-transferase inhibitor complex
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
Chem-1KM / : / 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 1.1Dec 4, 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.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)33,6056
Polymers32,9772
Non-polymers6284
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-58 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.475, 64.477, 83.907
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-1KM / (2R)-2-azanyl-3-[(1R,2S)-2-oxidanyl-1-phosphono-propyl]sulfanyl-propanoic acid


Mass: 259.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14NO6PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
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: 1.127 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: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 30311 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.084 / Χ2: 0.774 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.834.40.60127850.742192.7
1.83-1.914.70.45230100.811199.7
1.91-1.994.80.30430090.8421100
1.99-2.14.80.22130050.9281100
2.1-2.234.90.17129930.8171100
2.23-2.44.80.14530510.9071100
2.4-2.644.90.11330340.9051100
2.64-3.034.80.07930630.791100
3.03-3.814.80.06231070.591100
3.81-504.60.04832540.415199.8

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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: SAD / Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2468 / WRfactor Rwork: 0.1909 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8216 / SU B: 2.899 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1217 / SU Rfree: 0.1261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1530 5.1 %RANDOM
Rwork0.183 ---
obs0.1856 30257 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.52 Å2 / Biso mean: 26.3715 Å2 / Biso min: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å2-0 Å20 Å2
2---1.78 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 32 135 2493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022445
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.9513306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.39223.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78315421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4071519
X-RAY DIFFRACTIONr_chiral_restr0.1490.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021921
LS refinement shellResolution: 1.772→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 101 -
Rwork0.294 1788 -
all-1889 -
obs--90.56 %

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