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- PDB-5je5: Crystal structure of Burkholderia glumae ToxA with bound S-adenos... -

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Basic information

Entry
Database: PDB / ID: 5je5
TitleCrystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) and 1-demethyltoxoflavin
ComponentsMethyl transferase
KeywordsTRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / Product / Complex
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Chem-AZ9 / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Function and homology information
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.564 Å
AuthorsFenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM73220 United States
Robert A. Welch FoundationA-0034 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
CitationJournal: Biochemistry / Year: 2016
Title: Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis.
Authors: Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3833
Polymers27,8191
Non-polymers5642
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.539, 45.539, 96.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Methyl transferase / Methyltransferase / Putative ubiquinone/menaquinone biosynthesis methyltransferase / TRP-1


Mass: 27819.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Gene: toxA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LBJ0
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-AZ9 / 6-methylpyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione / 1-demethyltoxoflavin


Mass: 179.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: Rod
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 18 - 23% polyethylene glycol monomethyl ether 2000, 100 mM Tris, pH 6.1 - 6.8, 6 mM SAH, and 2 mM 1-demethyltoxoflavin
PH range: 6.1 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 1.56→18.6 Å / Num. obs: 31081 / % possible obs: 97.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.036 / Net I/av σ(I): 34.8 / Net I/σ(I): 22
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.5 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX(1.10-2155-000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Burkholderia glumae ToxA with bound SAH and 1,6-didemethyltoxoflavin

Resolution: 1.564→18.567 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.44
Details: SURFACE RESIDUE CYS236 SHOWS RESIDUAL ELECTRON DENSITY NEAR THE SULFUR ATOM AND IS POSSIBLY PARTIALLY OXIDIZED.
RfactorNum. reflection% reflection
Rfree0.1699 1515 4.88 %
Rwork0.1444 --
obs0.1456 31048 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.564→18.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 39 337 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092165
X-RAY DIFFRACTIONf_angle_d1.0972953
X-RAY DIFFRACTIONf_dihedral_angle_d15.21268
X-RAY DIFFRACTIONf_chiral_restr0.066295
X-RAY DIFFRACTIONf_plane_restr0.007397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5643-1.61480.21741150.17862609X-RAY DIFFRACTION96
1.6148-1.67250.23921420.17292698X-RAY DIFFRACTION99
1.6725-1.73940.19141340.16712712X-RAY DIFFRACTION100
1.7394-1.81850.19541800.16322697X-RAY DIFFRACTION100
1.8185-1.91430.20761290.16022697X-RAY DIFFRACTION99
1.9143-2.03410.19761470.15912687X-RAY DIFFRACTION99
2.0341-2.19090.15661560.14482729X-RAY DIFFRACTION100
2.1909-2.41090.18671310.14592694X-RAY DIFFRACTION99
2.4109-2.75880.17861480.14392697X-RAY DIFFRACTION100
2.7588-3.47210.1562940.13632761X-RAY DIFFRACTION99
3.4721-18.56820.13391390.12672552X-RAY DIFFRACTION94
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)
16.23770.583-5.67054.1828-1.59659.3110.16680.1812-0.1692-0.34220.00150.24490.0734-0.2749-0.16220.12990.027-0.06730.1417-0.01130.1841-7.48778.000612.4208
27.21785.73160.50486.43410.29232.41460.2701-0.21050.0180.4209-0.11760.0593-0.2191-0.0436-0.15650.17760.0090.03090.13010.00570.1018-2.695113.367228.4624
32.0399-1.04370.37284.69941.6192.76120.107-0.11250.17750.12040.04550.1186-0.3454-0.1574-0.13330.17430.02840.06040.09880.02540.1629-4.296823.940619.6179
47.4706-6.1517-2.69679.13826.43517.74030.14910.5068-0.2603-0.0703-0.3590.87150.001-0.55030.2120.15320.0351-0.02230.16760.03960.2406-11.72919.18259.014
51.9298-0.55870.13661.865-0.34841.53980.17760.22020.2716-0.1739-0.1509-0.2202-0.24910.2917-0.02990.1663-0.01750.05060.16710.02090.14726.751720.486413.2532
61.23220.3733-0.14852.3133-0.47761.81690.06280.0391-0.0592-0.0924-0.057-0.08470.15150.17940.00150.09390.0229-0.01350.1295-0.00060.07725.72234.475818.7279
77.49797.5587-4.49058.716-5.13523.25550.4254-0.35320.46940.6891-0.2040.2074-0.52520.1409-0.22920.2301-0.0785-0.02010.2325-0.0070.14065.414212.394131.8699
84.69453.1723-1.30184.3518-2.60973.03230.1059-0.23220.13590.1387-0.0050.1507-0.0350.0084-0.07850.10720.0064-0.00950.1396-0.01680.07241.68344.646230.2986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 133 )
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 222 )
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 245 )

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