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- PDB-5jdy: Crystal structure of Burkholderia glumae ToxA Y7F mutant with bou... -

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Basic information

Entry
Database: PDB / ID: 5jdy
TitleCrystal structure of Burkholderia glumae ToxA Y7F mutant with bound S-adenosylhomocysteine (SAH) and toxoflavin
ComponentsMethyl transferase
KeywordsTRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / Mutant / Product complex / Toxin
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Chem-TOF / Methyltransferase
Function and homology information
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 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
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8847
Polymers55,6072
Non-polymers1,2775
Water16,520917
1
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3813
Polymers27,8031
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5034
Polymers27,8031
Non-polymers7003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.185, 71.170, 78.151
Angle α, β, γ (deg.)90.00, 100.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27803.277 Da / Num. of mol.: 2 / Mutation: Y7F
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.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-TOF / 1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione / Toxoflavin


Mass: 193.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O2 / Comment: antibiotic, toxin*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / 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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: Rod/Needle
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 1 mM toxoflavin
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: 1.77→19.8 Å / Num. obs: 46227 / % possible obs: 97.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 / Net I/av σ(I): 16 / Net I/σ(I): 14.4
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.7 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX(1.10-2155-000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Burkholderia glumae ToxA Y7F mutant with bound SAH

Resolution: 1.77→19.764 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.35
RfactorNum. reflection% reflection
Rfree0.194 2311 5.01 %
Rwork0.1477 --
obs0.15 46170 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→19.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 88 917 4845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084303
X-RAY DIFFRACTIONf_angle_d0.9235863
X-RAY DIFFRACTIONf_dihedral_angle_d15.1262521
X-RAY DIFFRACTIONf_chiral_restr0.057584
X-RAY DIFFRACTIONf_plane_restr0.006786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7665-1.80260.21251210.15642204X-RAY DIFFRACTION82
1.8026-1.84170.24571370.17292548X-RAY DIFFRACTION97
1.8417-1.88450.26241620.17712634X-RAY DIFFRACTION98
1.8845-1.93160.33351350.25942580X-RAY DIFFRACTION99
1.9316-1.98380.21241170.17452679X-RAY DIFFRACTION99
1.9838-2.04210.1861390.14612622X-RAY DIFFRACTION99
2.0421-2.1080.17561320.13432630X-RAY DIFFRACTION99
2.108-2.18320.16821510.13472600X-RAY DIFFRACTION99
2.1832-2.27050.22981470.1952605X-RAY DIFFRACTION98
2.2705-2.37370.2121220.15712607X-RAY DIFFRACTION97
2.3737-2.49860.17071370.13582638X-RAY DIFFRACTION98
2.4986-2.65480.17581480.13932589X-RAY DIFFRACTION98
2.6548-2.85920.19681460.13722587X-RAY DIFFRACTION97
2.8592-3.14590.1771260.13792585X-RAY DIFFRACTION97
3.1459-3.59880.17321320.12992604X-RAY DIFFRACTION97
3.5988-4.52510.1661330.11482578X-RAY DIFFRACTION95
4.5251-19.76560.14931260.12472569X-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)
10.264-0.28720.23542.92621.8122.76690.06360.0465-0.0282-0.12750.001-0.0936-0.06460.0183-0.05890.01880.0054-0.00310.05590.00310.062419.898919.998.045
21.5074-0.20870.19480.65510.36621.0397-0.0103-0.0575-0.09630.01930.0133-0.04790.03650.0579-0.00180.034-0.0026-0.010.04160.01350.051724.373211.209517.1841
30.7279-0.11990.04570.5828-0.25031.1809-0.02270.0341-0.0911-0.00910.0090.0462-0.0053-0.09420.01260.03420.00130.00320.0393-0.01980.05296.86118.227813.8978
40.70910.1022-0.15112.1946-2.01572.65460.0348-0.0620.04820.1516-0.03660.0188-0.23920.12160.01260.04730.0053-0.00420.0461-0.01110.04313.755730.793215.0359
50.66620.10830.6770.64780.41053.35130.0780.09530.0841-0.11930.0541-0.0145-0.2070.172-0.10430.05810.01030.01380.05950.00650.07410.527755.776320.8304
61.298-0.31440.9920.5127-0.33152.06660.0178-0.0512-0.02680.01260.0308-0.1074-0.04070.1219-0.0380.02470.0016-0.00620.0529-0.00470.06228.81445.224425.657
77.5977-0.75382.36091.6233-0.90193.2358-0.1130.36250.0794-0.26560.0577-0.06310.00190.08880.06150.08760.00950.00170.056-0.00630.04169.504947.131711.1766
81.3105-0.0612-0.49790.5276-0.07360.5556-0.03230.0722-0.1415-0.0096-0.01090.03690.0655-0.05220.03950.0515-0.0033-0.01660.0415-0.00870.0423-4.359339.199822.9932
90.8796-0.10820.13011.2551-0.18890.9253-0.01420.04810.1126-0.1158-0.01350.1111-0.0791-0.05570.0230.0607-0.0048-0.01790.0392-0.00570.0455-11.304155.670322.9313
101.065-0.2597-0.04180.9829-0.81552.0446-0.01590.0570.005-0.1450.02430.17010.0085-0.1081-0.02770.0592-0.0122-0.03560.0335-0.00590.0647-14.256348.661225.1685
111.94872.0534-0.22172.2603-0.32680.74710.121-0.07050.00570.3503-0.1082-0.2352-0.01430.04960.00960.05860.0068-0.0110.0399-0.00660.0856-4.01153.832237.172
120.78690.6727-0.38363.26040.27250.63620.0691-0.01470.0787-0.0395-0.0808-0.0864-0.0628-0.01310.02820.0512-0.0006-0.01430.0361-0.00790.0519-6.0861.358731.9752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 245 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 35 )
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 71 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 85 )
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 133 )
9X-RAY DIFFRACTION9chain 'B' and (resid 134 through 184 )
10X-RAY DIFFRACTION10chain 'B' and (resid 185 through 203 )
11X-RAY DIFFRACTION11chain 'B' and (resid 204 through 222 )
12X-RAY DIFFRACTION12chain 'B' and (resid 223 through 245 )

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