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- PDB-5je1: Crystal structure of Burkholderia glumae ToxA with bound S-adenos... -

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Basic information

Entry
Database: PDB / ID: 5je1
TitleCrystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) and toxoflavin
ComponentsMethyl transferase
KeywordsTRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 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)56,7946
Polymers55,6392
Non-polymers1,1554
Water11,620645
1
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3973
Polymers27,8191
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3973
Polymers27,8191
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.699, 45.567, 74.907
Angle α, β, γ (deg.)90.00, 98.98, 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: 27819.277 Da / Num. of mol.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.08 Å3/Da / Density % sol: 40.91 % / 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 1 mM toxoflavin
PH range: 6.1 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→38.8 Å / Num. obs: 32328 / % possible obs: 95.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.103 / Net I/av σ(I): 9.9 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.5 / % possible all: 83.1

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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: 1.95→38.799 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.27
RfactorNum. reflection% reflection
Rfree0.2062 1619 5.01 %
Rwork0.146 --
obs0.1491 32310 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→38.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 80 645 4596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074084
X-RAY DIFFRACTIONf_angle_d0.8585544
X-RAY DIFFRACTIONf_dihedral_angle_d13.2152360
X-RAY DIFFRACTIONf_chiral_restr0.053565
X-RAY DIFFRACTIONf_plane_restr0.005726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9486-2.00590.30711250.21782093X-RAY DIFFRACTION79
2.0059-2.07070.24851450.19422481X-RAY DIFFRACTION93
2.0707-2.14470.24661270.17692638X-RAY DIFFRACTION99
2.1447-2.23050.23651430.16722620X-RAY DIFFRACTION99
2.2305-2.3320.20331440.16642624X-RAY DIFFRACTION99
2.332-2.4550.23151170.15332639X-RAY DIFFRACTION99
2.455-2.60870.25631220.1562650X-RAY DIFFRACTION98
2.6087-2.81010.21231100.15052650X-RAY DIFFRACTION98
2.8101-3.09280.21821450.14152584X-RAY DIFFRACTION97
3.0928-3.54010.18721490.12822586X-RAY DIFFRACTION96
3.5401-4.45910.16511520.1062543X-RAY DIFFRACTION95
4.4591-38.80680.1561400.12832583X-RAY DIFFRACTION93
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)
16.45671.30545.48034.03011.55647.7476-0.07630.28760.0269-0.40660.0886-0.0410.30590.1755-0.07870.133-0.00540.04930.11160.02180.093552.465320.510635.3118
21.56020.22730.83021.56911.39161.56220.0265-0.1734-0.1430.02450.025-0.02730.10160.017-0.01140.10470.00340.00910.06730.03280.090946.309714.02451.0779
31.3018-0.19011.25732.611-1.58395.28940.0949-0.0434-0.2030.0540.16920.09770.18460.0194-0.21890.09320.00040.00450.0552-0.00840.105645.30038.006345.1737
45.1319-2.30870.91557.0805-3.75946.10930.02170.3804-0.2138-0.4854-0.3251-0.52260.3910.50750.23380.19710.02180.05790.1173-0.0120.112350.41217.771434.376
52.64810.0610.30731.4674-0.72732.84150.00580.1191-0.1207-0.0910.00010.34120.1033-0.2584-0.02630.1247-0.031-0.05010.0925-0.0120.162536.16849.932239.1978
62.37570.5757-0.2472.1019-0.16211.3515-0.01670.06260.136-0.0711-0.00470.1206-0.1549-0.12340.01290.08750.0234-0.02250.0789-0.00060.055441.696528.159844.9092
75.38310.25291.6561.64890.21071.8325-0.1183-0.3076-0.01390.18260.02190.0177-0.0353-0.08010.0720.11030.0516-0.00780.0889-0.02520.073948.226925.993457.1458
83.29721.40274.93816.22290.93368.5932-0.17090.61680.6759-0.4143-0.0005-0.3037-0.54080.59270.19490.28690.00810.03790.24540.02830.151981.029119.093256.2782
92.31131.41621.48173.7717-0.93445.7407-0.11480.1027-0.106-0.27240.1598-0.06880.23210.0107-0.07310.05450.0136-0.03230.1202-0.02960.140866.161214.00464.8047
103.0997-1.4529-1.22592.56220.34552.8658-0.1808-0.09840.2999-0.0070.09790.1721-0.0804-0.18720.05180.07650.0142-0.03110.0875-0.01730.147372.620724.090571.6634
116.0501-6.7168-0.28578.34360.63014.50080.38630.78320.5575-0.9283-0.19620.0082-0.4891-0.2915-0.08150.21560.01820.00140.14550.10220.276981.170330.35962.7139
121.7132-0.40240.41071.50620.13871.30770.06680.1307-0.0524-0.0591-0.0266-0.086-0.06390.0719-0.05340.05810.007-0.00870.09530.00450.075480.50759.527668.2551
132.1982-0.00652.48191.10230.07744.31140.1109-0.0603-0.1515-0.0802-0.0310.2647-0.0892-0.2592-0.06140.06940-0.02450.1201-0.01280.158166.13455.595464.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 245 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 21 )
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 85 )
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 203 )
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 245 )

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