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- PDB-4ir0: Crystal Structure of Metallothiol Transferase FosB 2 from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4ir0
TitleCrystal Structure of Metallothiol Transferase FosB 2 from Bacillus anthracis str. Ames
ComponentsMetallothiol transferase FosB 2
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / 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 / Metallothiol transferase FosB 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsMaltseva, N. / Kim, Y. / Jedrzejczak, R. / Zhang, R. / 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. / Zhang, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 3UH9
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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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)36,23610
Polymers35,5812
Non-polymers6558
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-97 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.241, 48.241, 147.630
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: 17790.570 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): BL21 magic
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 10.7% PEG 3000, 50mM Tris pH7.6, 8.6% PEG2000 MME, 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: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 1.6→50 Å / Num. all: 43924 / Num. obs: 43924 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2059 / Rsym value: 0.543 / % possible all: 93.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIX(phenix.refine: dev_1227)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→34.449 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2229 5.08 %random
Rwork0.184 ---
all0.187 43857 --
obs0.187 43857 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 34 197 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042555
X-RAY DIFFRACTIONf_angle_d0.9493454
X-RAY DIFFRACTIONf_dihedral_angle_d15.739984
X-RAY DIFFRACTIONf_chiral_restr0.067366
X-RAY DIFFRACTIONf_plane_restr0.003450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6007-1.63550.28811540.29162445259989
1.6355-1.67350.31071410.29112586272793
1.6735-1.71530.31221350.27552627276295
1.7153-1.76170.27931490.2782544269394
1.7617-1.81350.27431380.26652639277795
1.8135-1.8720.25671520.25512582273494
1.872-1.93880.2631640.23722597276194
1.9388-2.01640.23451150.22792648276396
2.0164-2.10810.20691320.21532631276395
2.1081-2.21910.2121430.20552590273395
2.2191-2.35790.2231360.21372651278795
2.3579-2.53960.21791370.21882649278695
2.5396-2.79460.18851430.19512591273495
2.7946-3.19750.22251280.17322644277295
3.1975-4.02310.16151280.14492652278095
4.0231-19.95690.16061200.13952540266091
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)
12.4901-0.3223-0.80431.53211.30094.0651-0.0941-0.2708-0.1725-0.0196-0.0097-0.32160.47020.30580.07690.18420.03120.04950.18020.05120.291610.261919.4315110.6153
23.0540.25340.31552.17640.75893.5164-0.1165-0.1955-0.3363-0.0041-0.1943-0.01290.6132-0.14770.27690.2292-0.00440.09790.1692-0.00770.26183.234117.4537109.4556
31.6962-0.5323-0.0133.3516-0.51290.2611-0.04540.1664-0.0455-0.6526-0.0313-0.42170.0301-0.02080.06910.3962-0.01370.12010.1135-0.00990.32369.720923.40192.7113
45.5762-4.6927-0.2297.06640.74331.06630.09160.6179-0.4562-0.4677-0.37450.53370.5488-0.52370.24240.3647-0.01810.05470.1962-0.080.3365-0.307621.046191.3348
53.1085-0.4772-0.66474.3136-0.20573.9415-0.04750.2180.0355-0.4737-0.2133-0.01420.0025-0.10240.24790.21450.00890.04060.1245-0.03520.24362.71425.55894.8696
69.3552-0.86745.39684.8439-4.45126.35970.34991.1620.5421-0.4456-0.1086-0.30970.1559-0.6043-0.0780.45780.156-0.09040.58870.1230.3454-4.801444.30591.1239
76.7186-0.55241.42055.59971.00935.9769-0.1999-0.81860.65840.2820.3992-0.6404-0.57680.6422-0.04050.1998-0.0648-0.06260.3513-0.07720.3617-11.857763.874185.0417
83.3850.1107-0.65712.84670.44763.01590.0529-0.0710.2523-0.2615-0.25920.2022-0.2137-0.54140.16240.17360.0736-0.05080.2455-0.06690.2987-6.323433.6414106.511
92.6855-0.9506-0.79142.33340.49272.0551-0.1761-0.58470.07680.3422-0.0609-0.05870.41060.05590.20940.18440.00520.0250.3082-0.01030.23943.481525.93123.3364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 135 )
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 146 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 58 )
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 135 )

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