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- PDB-5je2: Crystal structure of Burkholderia glumae ToxA Y7F mutant with bou... -

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Basic information

Entry
Database: PDB / ID: 5je2
TitleCrystal structure of Burkholderia glumae ToxA Y7F 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: 1.519 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 11, 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

Downloads & links

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Assembly

Deposited unit
A: Methyl transferase
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,12010
Polymers55,6072
Non-polymers1,5148
Water17,583976
1
A: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5385
Polymers27,8031
Non-polymers7354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint6 kcal/mol
Surface area10730 Å2
MethodPISA
2
B: Methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5825
Polymers27,8031
Non-polymers7794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint4 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.936, 70.974, 77.754
Angle α, β, γ (deg.)90.00, 100.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 984 molecules

#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / 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: 2.19 Å3/Da / Density % sol: 43.89 % / 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, 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: 1.519→29.123 Å / Num. obs: 73380 / % possible obs: 99.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.036 / Net I/av σ(I): 30.1 / Net I/σ(I): 22.2
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 9.1 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Burkholderia glumae ToxA

Resolution: 1.519→29.123 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 13.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1538 3610 4.92 %
Rwork0.1278 --
obs0.1291 73355 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.519→29.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 98 976 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084315
X-RAY DIFFRACTIONf_angle_d1.0175867
X-RAY DIFFRACTIONf_dihedral_angle_d13.9732549
X-RAY DIFFRACTIONf_chiral_restr0.061588
X-RAY DIFFRACTIONf_plane_restr0.007788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5188-1.53880.18581210.14522360X-RAY DIFFRACTION87
1.5388-1.55990.17961330.13292575X-RAY DIFFRACTION95
1.5599-1.58210.16361290.12212694X-RAY DIFFRACTION100
1.5821-1.60580.14091210.11822709X-RAY DIFFRACTION100
1.6058-1.63080.16831230.12072665X-RAY DIFFRACTION100
1.6308-1.65760.161360.12062724X-RAY DIFFRACTION100
1.6576-1.68620.12831250.12332706X-RAY DIFFRACTION100
1.6862-1.71680.16271560.12452699X-RAY DIFFRACTION100
1.7168-1.74980.15891440.12682671X-RAY DIFFRACTION100
1.7498-1.78550.14611390.13212723X-RAY DIFFRACTION100
1.7855-1.82440.16811510.13322653X-RAY DIFFRACTION100
1.8244-1.86680.17941630.13232706X-RAY DIFFRACTION100
1.8668-1.91350.15731310.1362684X-RAY DIFFRACTION100
1.9135-1.96520.15011340.12882697X-RAY DIFFRACTION100
1.9652-2.0230.14651350.12932715X-RAY DIFFRACTION100
2.023-2.08830.15121390.12992693X-RAY DIFFRACTION100
2.0883-2.16290.15211580.12562711X-RAY DIFFRACTION100
2.1629-2.24950.13581540.12462684X-RAY DIFFRACTION100
2.2495-2.35180.16781180.13052715X-RAY DIFFRACTION100
2.3518-2.47570.15861360.13512701X-RAY DIFFRACTION100
2.4757-2.63080.18861670.13782695X-RAY DIFFRACTION100
2.6308-2.83370.17591530.13712691X-RAY DIFFRACTION100
2.8337-3.11860.14991340.13632698X-RAY DIFFRACTION99
3.1186-3.56920.14681350.12332702X-RAY DIFFRACTION99
3.5692-4.49410.13431450.10782727X-RAY DIFFRACTION99
4.4941-29.12820.12151300.12812747X-RAY DIFFRACTION98
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)
10.459-0.3946-0.05830.9984-0.19131.62210.01820.041-0.0191-0.0284-0.0063-0.0439-0.05750.0477-0.00090.0085-0.0074-0.00140.0486-0.00350.046621.67518.456312.0028
22.40980.34520.19971.5250.32791.2023-0.0007-0.0152-0.13630.00840.0254-0.0860.01850.0825-0.01640.02640.0072-0.00570.04240.00150.039927.29149.416314.4133
31.2808-0.07610.55470.5805-0.01291.62080.0122-0.0226-0.0890.0384-0.02540.02880.03920.0063-0.00040.02660.00340.00810.0296-0.00710.035112.04215.411720.5855
40.79970.1747-0.41110.6728-0.42951.111-0.00340.043-0.00930.0218-0.00620.0251-0.0364-0.00250.01060.02290.0169-0.00470.0389-0.00570.03999.224323.767811.8456
50.7368-0.23130.25171.15310.05751.35880.0280.03690.0575-0.0742-0.0087-0.0563-0.0910.04570.00640.0218-0.00280.0110.0418-0.0010.04222.589951.678722.6217
62.072-0.03140.37161.1851-0.34031.8650.00760.09440.0347-0.0414-0.0145-0.0436-0.05860.1604-0.00160.02740.0030.00590.0327-0.00440.03229.235246.191218.0757
71.10130.0855-0.51010.628-0.06390.6354-0.01860.0665-0.1122-0.002-0.01290.0490.0524-0.04410.02590.0413-0.0015-0.00870.0332-0.00570.0392-3.906938.638722.8448
80.54250.0681-0.03171.03430.08630.4975-0.00460.02580.0468-0.04590.00120.0315-0.0369-0.03490.00680.03690.00270.00150.0337-0.00110.0329-9.411754.725827.4785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 156 )
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 245 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 85 )
7X-RAY DIFFRACTION7chain 'B' and (resid 86 through 133 )
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 245 )

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