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

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Basic information

Entry
Database: PDB / ID: 5jdz
TitleCrystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH)
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 / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Function and homology information
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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)56,4074
Polymers55,6392
Non-polymers7692
Water9,944552
1
A: Methyl transferase
B: Methyl transferase
hetero molecules

A: Methyl transferase
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8158
Polymers111,2774
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+3/2,-y+1,z-1/21
2
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers27,8191
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers27,8191
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.839, 65.627, 144.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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 Å3/Da / Density % sol: 38.47 % / Description: Plate
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, and 6 mM SAH
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: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.6→39.3 Å / Num. obs: 56573 / % possible obs: 94.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Net I/av σ(I): 21.4 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.7 / % possible all: 84.8

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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: FOURIER SYNTHESIS
Starting model: Burkholderia glumae ToxA Y7A mutant with bound SAH

Resolution: 1.6→39.3 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.97
Details: THERE IS RESIDUAL ACTIVE SITE ELECTRON DENSITY WHICH WE WERE UNABLE TO RELIABLY MODEL.
RfactorNum. reflection% reflection
Rfree0.2136 2764 4.89 %
Rwork0.177 --
obs0.1788 56499 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 52 552 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053824
X-RAY DIFFRACTIONf_angle_d0.8085183
X-RAY DIFFRACTIONf_dihedral_angle_d11.5722224
X-RAY DIFFRACTIONf_chiral_restr0.053533
X-RAY DIFFRACTIONf_plane_restr0.005677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5992-1.62680.28021150.22472159X-RAY DIFFRACTION77
1.6268-1.65630.22431150.21572499X-RAY DIFFRACTION88
1.6563-1.68820.25551460.20872463X-RAY DIFFRACTION88
1.6882-1.72270.27281220.21562514X-RAY DIFFRACTION90
1.7227-1.76010.25261300.21442505X-RAY DIFFRACTION90
1.7601-1.80110.2421210.20172582X-RAY DIFFRACTION91
1.8011-1.84610.21971280.1922585X-RAY DIFFRACTION92
1.8461-1.8960.23081290.19092636X-RAY DIFFRACTION93
1.896-1.95180.23441440.19132700X-RAY DIFFRACTION95
1.9518-2.01480.2071560.18992693X-RAY DIFFRACTION96
2.0148-2.08680.27411490.19392705X-RAY DIFFRACTION97
2.0868-2.17040.23851470.18722784X-RAY DIFFRACTION98
2.1704-2.26910.25161320.1852803X-RAY DIFFRACTION98
2.2691-2.38870.25871530.18342812X-RAY DIFFRACTION99
2.3887-2.53840.22591290.18942867X-RAY DIFFRACTION100
2.5384-2.73430.21711590.18652832X-RAY DIFFRACTION99
2.7343-3.00940.22151550.17892848X-RAY DIFFRACTION99
3.0094-3.44460.18021500.16792878X-RAY DIFFRACTION100
3.4446-4.3390.17711450.14372908X-RAY DIFFRACTION99
4.339-39.3330.17271390.15932962X-RAY DIFFRACTION96
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)
17.0148-2.43044.07854.5318-3.20573.2841-0.0631-0.02281.0293-0.01180.21470.8868-1.6331-2.0825-0.12550.77020.1803-0.02520.82010.0931.003120.513743.933380.5099
21.83630.43380.04771.7401-0.48661.965-0.02050.07750.14310.03010.14130.1408-0.0222-0.2408-0.06840.08660.0056-0.00830.12410.02470.11626.219431.219183.7998
32.5668-0.07660.15650.4652-0.47192.0373-0.0748-0.4885-0.32460.041-0.06750.03190.24880.25110.03780.14790.02960.03630.14830.05990.157926.742628.252950.3457
43.8762-1.57321.05816.4867-2.28824.3691-0.0578-0.34120.02270.2101-0.0146-0.340.13050.33680.02120.09160.02760.01440.14350.02610.108333.472330.012246.596
52.9042-1.87723.38937.9292-1.6416.9716-0.1969-0.07790.81380.35640.048-0.8241-1.06010.73450.17160.225-0.07750.02880.2334-0.01110.341638.385140.482442.7236
63.11050.062-0.1924.0083-1.13492.0845-0.25090.4511-0.3335-0.49430.1769-0.31320.27660.0840.04260.20620.03110.09390.18980.00010.167432.35928.652135.6758
74.6784-1.15012.12125.107-0.18764.8089-0.06550.4337-0.2635-0.3457-0.09420.3647-0.058-0.31860.15780.1129-0.01750.01310.1659-0.02980.113318.772929.088236.1366
81.7266-0.57350.59254.22490.65112.4836-0.1822-0.0952-0.3830.0046-0.01180.41250.1479-0.27650.1470.1375-0.02220.05990.08320.0020.20514.217130.379946.7868
93.79821.39393.62164.22872.23615.1537-0.02370.43750.2203-0.18010.04130.3904-0.7514-0.1560.17130.18090.0830.01290.2359-0.01770.22239.020144.035145.6812
103.865-0.6919-1.02326.41530.75093.51450.07110.32780.033-0.2485-0.06530.0857-0.2795-0.39590.01070.14580.05610.00170.1996-0.00290.086511.932236.803841.0796
112.65640.47050.99616.49634.75253.6271-0.1445-0.4526-0.52890.4747-0.1455-0.08870.7973-0.30380.29030.2299-0.04240.08690.15410.01430.253314.612125.498554.4974
122.6308-0.08870.40942.92721.56934.9629-0.1967-0.525-0.15840.5740.1738-0.04720.235-0.34410.04150.21520.03550.04810.20810.02970.175612.36533.068656.6089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 245 )
3X-RAY DIFFRACTION3chain 'B' and (resid 23 through 51 )
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 71 )
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 85 )
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 106 )
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 133 )
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 156 )
9X-RAY DIFFRACTION9chain 'B' and (resid 157 through 171 )
10X-RAY DIFFRACTION10chain 'B' and (resid 172 through 204 )
11X-RAY DIFFRACTION11chain 'B' and (resid 205 through 222 )
12X-RAY DIFFRACTION12chain 'B' and (resid 223 through 245 )

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