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- PDB-5ufm: Crystal structure of Burkholderia thailandensis 1,6-didemethyltox... -

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Basic information

Entry
Database: PDB / ID: 5ufm
TitleCrystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound 1,6-didemethyltoxoflavin and S-adenosylhomocysteine
ComponentsMethyltransferase domain protein
KeywordsTRANSFERASE / N-methyltransferase / S-adenosylmethionine-dependent
Function / homologyMethyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å
AuthorsFenwick, M.K. / Ealick, S.E. / Almabruk, K.H. / Begley, T.P. / Philmus, B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Oregon State University College of Pharmacy United States
CitationJournal: Biochemistry / Year: 2017
Title: Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase.
Authors: Fenwick, M.K. / Almabruk, K.H. / Ealick, S.E. / Begley, T.P. / Philmus, B.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase domain protein
B: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,31319
Polymers52,6812
Non-polymers2,63217
Water8,323462
1
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,94311
Polymers26,3401
Non-polymers1,60310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3708
Polymers26,3401
Non-polymers1,0307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-136 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.698, 112.698, 78.367
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyltransferase domain protein / Uncharacterized protein


Mass: 26340.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_II1283, DR63_4497 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2T5S0

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Non-polymers , 5 types, 479 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-AZ8 / pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione / 1,6-didemethyltoxoflavin


Mass: 165.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H3N5O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 100 mM HEPES, pH 6.0 - 7.0, 1.0 - 2.0 M ammonium sulfate, and 1 mM S-adenosylhomocysteine. 1,6-didemethyltoxoflavin (25 mM), S-adenosylhomocysteine (6 mM), and dithiothreitol (5 mM) were ...Details: 100 mM HEPES, pH 6.0 - 7.0, 1.0 - 2.0 M ammonium sulfate, and 1 mM S-adenosylhomocysteine. 1,6-didemethyltoxoflavin (25 mM), S-adenosylhomocysteine (6 mM), and dithiothreitol (5 mM) were added during crystal soak experiment.
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9759 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
ReflectionResolution: 1.77→23 Å / Num. obs: 54274 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Net I/av σ(I): 17.3 / Net I/σ(I): 12.6
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.83 / % possible all: 85.9

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Processing

Software
NameVersionClassification
HKL-2000v714data processing
PHENIX(1.11.1_2575: 000)refinement
Coot0.8.7model building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.77→23 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.36
RfactorNum. reflection% reflection
Rfree0.184 2665 4.92 %
Rwork0.1521 --
obs0.1537 54199 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 161 462 4138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063878
X-RAY DIFFRACTIONf_angle_d0.8815309
X-RAY DIFFRACTIONf_dihedral_angle_d21.3991407
X-RAY DIFFRACTIONf_chiral_restr0.055549
X-RAY DIFFRACTIONf_plane_restr0.006693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80120.32571010.25292220X-RAY DIFFRACTION79
1.8012-1.83590.27241220.24462559X-RAY DIFFRACTION93
1.8359-1.87330.28031400.22342747X-RAY DIFFRACTION100
1.8733-1.9140.23271450.20522760X-RAY DIFFRACTION100
1.914-1.95850.21021470.18442721X-RAY DIFFRACTION100
1.9585-2.00750.20871130.16552779X-RAY DIFFRACTION100
2.0075-2.06170.20731660.16622717X-RAY DIFFRACTION100
2.0617-2.12230.1731380.15822782X-RAY DIFFRACTION100
2.1223-2.19080.17521600.14652731X-RAY DIFFRACTION100
2.1908-2.2690.1761480.14242738X-RAY DIFFRACTION100
2.269-2.35980.19171650.15442739X-RAY DIFFRACTION100
2.3598-2.46710.17671290.15882763X-RAY DIFFRACTION100
2.4671-2.5970.20221460.15632764X-RAY DIFFRACTION100
2.597-2.75940.23371480.16392768X-RAY DIFFRACTION100
2.7594-2.97210.19961450.15222760X-RAY DIFFRACTION100
2.9721-3.27040.15011430.14122775X-RAY DIFFRACTION100
3.2704-3.74190.15481260.12892768X-RAY DIFFRACTION99
3.7419-4.70780.14791400.11962753X-RAY DIFFRACTION99
4.7078-23.03220.17061430.14882690X-RAY DIFFRACTION95
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)
18.2154-4.5764-1.72987.07381.13774.4679-0.2684-0.4278-0.82580.51590.32670.53380.6703-0.3977-0.08760.2101-0.0238-0.02320.24480.020.21827.784231.241126.4879
21.08740.66650.06891.79270.63291.80490.00160.1616-0.1086-0.04450.0802-0.01950.0891-0.023-0.03530.13660.0868-0.01010.2235-0.01970.142921.540641.028319.5998
31.01690.56350.04980.98880.38911.67080.05920.064-0.1235-0.07760.0959-0.15560.04480.2054-0.08560.12950.1068-0.00540.2448-0.03430.180731.695344.540716.0468
41.59010.42360.0550.98990.38191.38670.044-0.1189-0.0850.20880.0283-0.08410.1571-0.0138-0.05680.16620.0895-0.02660.21750.01690.160422.232438.983732.2333
50.8085-1.0952-0.46466.20452.54181.0488-0.02630.2119-0.0061-0.87620.26440.4628-0.8547-0.2395-0.14050.7270.0916-0.02020.31810.05680.251315.256278.476614.925
60.5278-0.11130.11151.6546-0.33910.926-0.0668-0.04920.01650.00860.10770.1749-0.1524-0.0851-0.04330.19170.09070.00580.1992-0.00410.155211.963266.560932.0087
74.6729-0.02121.79537.6494-2.23546.9308-0.079-0.1399-0.07270.23360.01960.38-0.0342-0.47390.06030.16840.08650.07880.23980.00120.24.75863.573941.624
80.8463-0.36250.88382.7647-0.83041.0534-0.0459-0.00760.08340.1050.0451-0.0254-0.15970.0293-0.01090.24270.08340.00070.1623-0.0210.14319.673275.292636.7787
93.1018-0.62441.33222.49280.21543.41630.04130.2390.1722-0.3845-0.0523-0.1109-0.0535-0.01370.01830.19940.04970.02810.1479-0.01190.14721.779373.637524.3693
104.12550.07331.20873.29252.37892.0490.02360.25780.2677-0.05040.0586-0.4165-0.15660.6751-0.09810.23660.01690.01410.24470.01360.250732.806874.177629.3492
112.63570.04941.0713.08841.23933.810.09110.0975-0.0995-0.00280.0319-0.25140.12130.2836-0.15820.18310.06810.0270.16760.00550.150226.86164.812926.563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 130 )
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 228 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 99 )
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 117 )
8X-RAY DIFFRACTION8chain 'B' and (resid 118 through 156 )
9X-RAY DIFFRACTION9chain 'B' and (resid 157 through 189 )
10X-RAY DIFFRACTION10chain 'B' and (resid 190 through 201 )
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 228 )

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