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- PDB-4jd1: Crystal Structure of Metallothiol Transferase FosB 2 from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4jd1
TitleCrystal Structure of Metallothiol Transferase FosB 2 from Bacillus anthracis str. Ames
ComponentsMetallothiol transferase FosB 2
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / cytosol / NIAID / National Institute of Allergy and Infectious Diseases / alpha/beta fold
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 / TRIETHYLENE GLYCOL / Metallothiol transferase FosB 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaltseva, N. / Kim, Y. / Jedrzejczak, R. / Sharma, S.V. / Hamilton, C.J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Metallothiol Transferase FosB 2 from Bacillus anthracis str. Ames
Authors: Maltseva, N. / Kim, Y. / Jedrzejczak, R. / Sharma, S.V. / Hamilton, C.J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif / 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_auth_seq_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_ref_seq_dif.details / _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 2
B: Metallothiol transferase FosB 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7637
Polymers35,2062
Non-polymers5575
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-96 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.157, 48.157, 147.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 17602.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS3818, BA_4109, fosB-2, fosB2, GBAA_4109 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: Q81W73, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4.3% PEG 2000, 50 mM Tris pH 8.0, 28.6% PEG550 MME, 20 mM BOH, 5 mM fosfomycin, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 1.7→50 Å / Num. all: 36837 / Num. obs: 36837 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 22.76 Å2 / Rsym value: 0.057 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1861 / Rsym value: 0.791 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1227)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR0

4ir0


Resolution: 1.7→34.414 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1830 5 %random
Rwork0.172 ---
all0.174 36564 --
obs0.174 36564 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 28 184 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112640
X-RAY DIFFRACTIONf_angle_d1.4463572
X-RAY DIFFRACTIONf_dihedral_angle_d19.4821002
X-RAY DIFFRACTIONf_chiral_restr0.107378
X-RAY DIFFRACTIONf_plane_restr0.007464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7005-1.74640.22531330.25782663279694
1.7464-1.79770.23971290.24562650277994
1.7977-1.85570.2461500.23592647279793
1.8557-1.92190.21181400.21692643278394
1.9219-1.99860.19611280.20282663279195
1.9986-2.08940.21951420.19742665280795
2.0894-2.19920.20291210.19712696281795
2.1992-2.33650.23151420.19642658280095
2.3365-2.51620.23141310.20062693282495
2.5162-2.7680.20861540.18132653280794
2.768-3.16530.21021510.16892680283195
3.1653-3.97570.17251440.14442687283195
3.9757-15.06660.15661580.12832687284594
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0171-0.4854-0.1392.592-0.59943.1639-0.11030.219-0.25090.0329-0.14270.14790.6575-0.04120.19230.2598-0.03670.07190.1666-0.03730.167916.1127-6.3572-2.4707
21.61270.7818-0.13282.0686-1.14340.8166-0.0584-0.236-0.03580.4601-0.03540.20530.080.09260.0880.3436-0.00020.08160.1253-0.00350.165915.8613-1.073114.8668
32.77211.80920.21316.11471.15392.1201-0.0014-0.38880.18190.5324-0.19110.00050.03230.37070.16250.2739-0.0338-0.00490.21230.02870.156223.73775.533814.3184
44.2599-0.79850.21280.6412-1.43844.7652-0.20860.57720.5228-0.05480.01540.0665-0.4177-0.91120.19690.32940.0995-0.13080.486-0.04050.320635.862838.585723.4085
52.0422.1156-1.60173.9889-1.52164.837-0.10070.02670.18720.3082-0.10460.2892-0.10340.1430.05680.1871-0.0191-0.02010.1279-0.0020.134321.69065.27875.5322
63.903-0.86412.64772.2717-0.23991.8534-0.03730.17070.3863-0.0748-0.2679-0.4087-0.22610.8450.13270.1629-0.0826-0.05090.45420.17530.339835.828612.0892-4.1741
73.221-0.5177-0.67532.38241.96071.64260.0269-0.08260.19170.3164-0.1422-0.3678-0.43910.43150.09580.2134-0.1143-0.05540.25270.06860.225729.538613.37292.3825
83.202-0.67230.63352.5086-0.13571.2133-0.02820.119-0.0047-0.0177-0.2335-0.42670.52230.43220.18560.21290.09850.07240.35430.09090.222529.6526-1.6344-4.4577
94.43091.5090.51982.5281.17150.5523-0.19040.49870.1018-0.3645-0.02760.05670.0435-0.01270.0870.1538-0.0170.00060.5130.14880.201327.510911.3786-19.9857
104.22770.784-0.22632.4032-0.33291.7398-0.1650.5381-0.0279-0.2859-0.1289-0.0560.3580.14620.22880.16810.0160.03530.29570.03540.149824.26441.6183-15.0443
118.69887.18644.38037.01783.05012.8479-0.27310.81130.2984-0.86040.20260.71920.3659-0.32370.12810.3765-0.1124-0.08710.4668-0.06270.29474.8423-2.3707-16.5011
121.23150.91840.37442.67080.57092.87990.4666-0.5230.48140.4679-0.40570.4003-0.5176-0.49330.44840.6790.0782-0.02230.442-0.24940.3358-13.9191-11.9722-24.0795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 147 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 14 )
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 72 )
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 85 )
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 120 )
11X-RAY DIFFRACTION11chain 'B' and (resid 121 through 133 )
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 147 )

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