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- PDB-5f6q: Crystal Structure of Metallothiol Transferase from Bacillus anthr... -

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Basic information

Entry
Database: PDB / ID: 5f6q
TitleCrystal Structure of Metallothiol Transferase from Bacillus anthracis str. Ames
ComponentsMetallothiol transferase FosB 2
KeywordsTRANSFERASE / alpha-beta fold / PSI-Biology / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
: / Metallothiol transferase FosB 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsMaltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Metallothiol Transferase from Bacillus anthracis str. Ames
Authors: Maltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallothiol transferase FosB 2
B: Metallothiol transferase FosB 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,48815
Polymers33,6422
Non-polymers84613
Water4,324240
1
A: Metallothiol transferase FosB 2
hetero molecules

A: Metallothiol transferase FosB 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,35112
Polymers33,6422
Non-polymers70910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area7060 Å2
ΔGint-158 kcal/mol
Surface area13630 Å2
MethodPISA
2
B: Metallothiol transferase FosB 2
hetero molecules

B: Metallothiol transferase FosB 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,62418
Polymers33,6422
Non-polymers98216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9280 Å2
ΔGint-269 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.873, 84.793, 109.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21B-415-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallothiol transferase FosB 2 / Fosfomycin resistance protein 2


Mass: 16821.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: fosB2, fosB-2, BA_4109, GBAA_4109, BAS3818 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q81W73, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Non-polymers , 6 types, 253 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate; 0.1M BIS-TRIS pH 6.5; 25% PEG 3350
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 60636 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rsym value: 0.08 / Net I/σ(I): 24.8
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.04 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JDI

4jdi


Resolution: 1.52→27.39 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.728 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16941 3077 5.1 %RANDOM
Rwork0.14517 ---
obs0.1464 57550 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.358 Å2
Baniso -1Baniso -2Baniso -3
1--17.89 Å20 Å20 Å2
2--1.86 Å20 Å2
3---16.02 Å2
Refinement stepCycle: 1 / Resolution: 1.52→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 36 240 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192521
X-RAY DIFFRACTIONr_bond_other_d0.0020.022395
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9563409
X-RAY DIFFRACTIONr_angle_other_deg0.89235514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49224.676139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70515468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9311515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02618
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.072.3971173
X-RAY DIFFRACTIONr_mcbond_other2.0412.3961172
X-RAY DIFFRACTIONr_mcangle_it2.4033.5991482
X-RAY DIFFRACTIONr_mcangle_other2.4133.5991483
X-RAY DIFFRACTIONr_scbond_it2.8012.7971348
X-RAY DIFFRACTIONr_scbond_other2.8032.7971348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1444.0481928
X-RAY DIFFRACTIONr_long_range_B_refined3.56720.292950
X-RAY DIFFRACTIONr_long_range_B_other3.38719.7192838
X-RAY DIFFRACTIONr_rigid_bond_restr1.76434916
X-RAY DIFFRACTIONr_sphericity_free25.388567
X-RAY DIFFRACTIONr_sphericity_bonded10.32655041
LS refinement shellResolution: 1.519→1.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 216 -
Rwork0.233 3851 -
obs--90.42 %

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