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- PDB-5je3: Crystal structure of Burkholderia glumae ToxA Y7A mutant with bou... -

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Basic information

Entry
Database: PDB / ID: 5je3
TitleCrystal structure of Burkholderia glumae ToxA Y7A mutant with bound S-adenosylhomocysteine (SAH)
ComponentsMethyl transferase
KeywordsTRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / Mutant / 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 / MOLECULAR REPLACEMENT / Resolution: 1.792 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)56,2234
Polymers55,4542
Non-polymers7692
Water9,944552
1
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1122
Polymers27,7271
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1122
Polymers27,7271
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.071, 67.265, 144.757
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: 27727.182 Da / Num. of mol.: 2 / Mutation: Y7A
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: 2.07 Å3/Da / Density % sol: 40.47 % / 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.79→33.7 Å / Num. obs: 43376 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.059 / Net I/av σ(I): 27 / Net I/σ(I): 16.6
Reflection shellResolution: 1.79→1.87 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7

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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: 1.792→33.694 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.11
RfactorNum. reflection% reflection
Rfree0.2111 2122 4.9 %
Rwork0.1656 --
obs0.1678 43335 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.792→33.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 52 552 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083728
X-RAY DIFFRACTIONf_angle_d0.9245054
X-RAY DIFFRACTIONf_dihedral_angle_d13.7992178
X-RAY DIFFRACTIONf_chiral_restr0.059516
X-RAY DIFFRACTIONf_plane_restr0.006662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7917-1.83340.25091100.22862128X-RAY DIFFRACTION77
1.8334-1.87920.29131480.20892732X-RAY DIFFRACTION100
1.8792-1.930.26081390.20522746X-RAY DIFFRACTION100
1.93-1.98680.22711340.19172749X-RAY DIFFRACTION100
1.9868-2.05090.22171350.1762791X-RAY DIFFRACTION100
2.0509-2.12420.20161460.17522738X-RAY DIFFRACTION100
2.1242-2.20930.25841690.16822731X-RAY DIFFRACTION100
2.2093-2.30980.1971290.17822787X-RAY DIFFRACTION100
2.3098-2.43150.22231390.17522759X-RAY DIFFRACTION100
2.4315-2.58380.23631320.18032814X-RAY DIFFRACTION100
2.5838-2.78320.23131580.17122780X-RAY DIFFRACTION100
2.7832-3.06310.2341470.17172790X-RAY DIFFRACTION100
3.0631-3.5060.18241560.15342815X-RAY DIFFRACTION100
3.506-4.41560.1871180.13482888X-RAY DIFFRACTION100
4.4156-33.70010.18471620.15922965X-RAY DIFFRACTION99
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)
14.7044-0.4194-0.13662.28650.98194.43940.02780.3572-0.0161-0.0883-0.05440.1295-0.0271-0.50360.01070.130.0019-0.02080.18180.00220.132617.237428.179780.3139
28.13321.01751.90936.60250.75438.2343-0.37540.09561.1459-0.10190.17430.7138-1.1227-0.49740.05370.28540.12940.03820.25750.0010.46169.028240.508685.9455
32.2728-0.38510.43235.3444-0.60835.2556-0.2371-0.4685-0.08970.52680.22810.4174-0.1725-0.3581-0.01540.18970.01180.06830.261-0.02640.181114.591329.025693.4328
44.3521.4973-0.73813.2515-1.14772.04-0.1191-0.00660.11710.0620.0347-0.14130.0060.12570.07350.13290.0062-0.01940.1364-0.0170.102929.886328.871288.0846
54.33620.77980.85794.2902-1.61962.4046-0.0593-0.34080.87720.2538-0.00380.3974-0.5044-0.0280.1560.2953-0.0504-0.03260.2353-0.04140.396735.673842.718784.7794
62.2607-1.14031.70053.6301-3.47833.27180.06510.1198-0.2078-0.14470.0116-0.02220.46980.389-0.11390.1470.01520.01450.1951-0.01320.183533.984524.003281.2986
72.3621-0.94741.04242.2699-1.72367.1734-0.04320.54380.4881-0.57630.20590.34140.14880.5532-0.11960.209-0.0485-0.02970.26640.03650.197534.469631.997372.4793
83.57020.47620.02931.7844-0.3523.65390.2338-0.8649-0.13450.0717-0.33840.00790.13870.1001-0.09310.182-0.0163-0.00710.27060.05780.144926.62727.582149.9556
94.10520.22740.42473.6617-1.0485.15040.0212-0.04620.1782-0.1738-0.1147-0.3441-0.10880.36350.09730.15660.01960.05160.11860.02350.175834.352532.228941.1523
104.7618-1.3678-0.58593.70410.86622.229-0.0341-0.1375-0.0018-0.1341-0.04320.14540.116-0.22260.06330.1736-0.0278-0.02110.15210.01430.11716.96728.913240.2372
112.4499-0.33142.24972.65051.24679.28840.0499-0.38960.41910.4102-0.30140.3235-0.77150.24960.31630.3277-0.12460.02680.2828-0.05510.29568.392543.503744.9011
122.777-1.0949-0.21712.0934-0.67134.48060.2043-0.15330.19790.1441-0.3044-0.12-0.36790.1720.07150.1888-0.0811-0.0460.21230.00740.181911.336136.024240.5866
131.1801-0.36980.48712.00681.1076.70370.0109-0.5968-0.2610.282-0.10230.05340.6977-0.2805-0.01570.2126-0.0670.00390.36140.06310.194214.625224.327953.5933
141.4293-0.24730.00092.01470.27945.4838-0.0962-0.4450.10870.5960.1729-0.01950.1455-0.5151-0.02070.202-0.02580.00020.36560.00590.16612.116732.102856.2301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 156 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 222 )
7X-RAY DIFFRACTION7chain 'A' and (resid 223 through 245 )
8X-RAY DIFFRACTION8chain 'B' and (resid 23 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 106 )
10X-RAY DIFFRACTION10chain 'B' and (resid 107 through 156 )
11X-RAY DIFFRACTION11chain 'B' and (resid 157 through 171 )
12X-RAY DIFFRACTION12chain 'B' and (resid 172 through 204 )
13X-RAY DIFFRACTION13chain 'B' and (resid 205 through 222 )
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 245 )

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