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- PDB-9c3t: Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV fr... -

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Basic information

Entry
Database: PDB / ID: 9c3t
TitleCrystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTAAAC as recognition sequence
Components
  • DNA1
  • DNA2
  • Methyltransferase
KeywordsDNA BINDING PROTEIN / DNA N6-Adenine Methyltransferase / M.BceJIV / Burkholderia cenocepacia
Function / homology
Function and homology information


N-methyltransferase activity / DNA restriction-modification system / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / DNA binding / cytoplasm
Similarity search - Function
Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / DNA / DNA (> 10) / Methyltransferase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKottur, J. / Quintana-Feliciano, R. / Aggarwal, A.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation.
Authors: Quintana-Feliciano, R. / Kottur, J. / Ni, M. / Ghosh, R. / Salas-Estrada, L. / Ahlsen, G. / Rechkoblit, O. / Shapiro, L. / Filizola, M. / Fang, G. / Aggarwal, A.K.
History
DepositionJun 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 25, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
D: Methyltransferase
E: DNA1
F: DNA2
G: DNA1
H: DNA2
I: DNA1
J: DNA2
K: DNA1
L: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,72316
Polymers160,19712
Non-polymers1,5264
Water6,233346
1
A: Methyltransferase
B: Methyltransferase
E: DNA1
F: DNA2
G: DNA1
H: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8618
Polymers80,0996
Non-polymers7632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-57 kcal/mol
Surface area23730 Å2
MethodPISA
2
C: Methyltransferase
D: Methyltransferase
I: DNA1
J: DNA2
K: DNA1
L: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8618
Polymers80,0996
Non-polymers7632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint-58 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.728, 137.728, 167.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
Methyltransferase


Mass: 31490.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: JAO13_04290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8I1DKW0
#2: DNA chain
DNA1


Mass: 4263.805 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)
#3: DNA chain
DNA2


Mass: 4294.814 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)
#4: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.10% w/v n-Octyl-beta-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, and 22% w/v Polyethylene glycol 3350
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.37→32.98 Å / Num. obs: 38837 / % possible obs: 94.1 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.2
Reflection shellResolution: 2.37→2.69 Å / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1944 / CC1/2: 0.594 / % possible all: 74.5

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Processing

Software
NameVersionClassification
PHENIX(1.20rc3_4406: ???)refinement
Aimless0.7.7data scaling
XDSJun 30, 2023 (BUILT 20230630)data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→32.76 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1950 5.02 %
Rwork0.1808 --
obs0.1834 38828 61.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7876 2269 0 346 10491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310751
X-RAY DIFFRACTIONf_angle_d0.60815081
X-RAY DIFFRACTIONf_dihedral_angle_d25.4592198
X-RAY DIFFRACTIONf_chiral_restr0.041624
X-RAY DIFFRACTIONf_plane_restr0.0051557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.2686160X-RAY DIFFRACTION
2.43-2.50.4624150.278211X-RAY DIFFRACTION
2.5-2.570.387330.3257448X-RAY DIFFRACTION
2.57-2.650.44500.3809X-RAY DIFFRACTION
2.65-2.750.3267570.29911259X-RAY DIFFRACTION30
2.75-2.860.2739921761X-RAY DIFFRACTION42
2.86-2.990.30931510.25952775X-RAY DIFFRACTION65
2.99-3.150.29332210.24513949X-RAY DIFFRACTION93
3.15-3.340.24032200.18584261X-RAY DIFFRACTION100
3.34-3.60.23612190.17144232X-RAY DIFFRACTION100
3.6-3.960.23092610.16634231X-RAY DIFFRACTION100
3.96-4.530.17992010.14494276X-RAY DIFFRACTION100
4.53-5.710.20792270.15054274X-RAY DIFFRACTION100
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)
10.05540.0663-0.02510.1473-0.06710.0319-0.0979-0.017-0.11010.0235-0.010.08630.11180.0037-0.2380.34140.04620.22460.0650.16790.387-16.1607-55.00357.5806
20.06420.03290.05480.01710.02790.0471-0.0053-0.0437-0.00690.0476-0.0180.0224-0.0153-0.0298-0.05430.3788-0.03430.16890.18420.03420.1658-12.5729-47.924815.8711
30.1474-0.01380.11510.0269-0.05720.1565-0.1329-0.146-0.07710.0769-0.0333-0.03560.01420.0906-0.49160.03650.2146-0.0466-0.15210.2435-0.0588-6.4697-40.75953.7577
40.18810.09230.1280.11170.01380.1347-0.01660.1433-0.157-0.16690.0577-0.081-0.04550.076-0.02970.39950.11790.09440.1438-0.05780.254811.4319-49.0688-10.4938
50.11090.111-0.0440.1237-0.02850.0412-0.2029-0.0166-0.1713-0.0795-0.01730.09770.2-0.0281-0.42280.3424-0.03450.1845-0.13030.02080.2608-9.5337-54.3304-5.1555
60.0817-0.06710.01890.11120.04390.06630.0294-0.05840.115-0.01110.0020.0267-0.10150.02830.06390.3031-0.029800.2015-0.17550.47085.8008-10.01249.9364
70.0572-0.0099-0.06230.00780.01050.07710.0006-0.28690.01710.16790.01910.05770.01080.18270.00790.21870.01290.01650.2143-0.04950.19064.6318-26.396211.9693
80.03090.0157-0.02030.14030.10940.12330.0196-0.0012-0.0042-0.0239-0.00780.02180.11650.1092-0.00650.0910.0966-0.0357-0.0060.05210.14171.9246-33.2977-0.1097
90.12820.0593-0.00790.0421-0.00030.00190.0046-0.0395-0.08430.0249-0.0022-0.00740.01160.02790.01470.13880.1942-0.05170.05070.02010.0522.2506-35.8711.8786
100.01940.0053-0.00610.01310.03450.1236-0.00750.00550.07740.00490.04910.1003-0.0412-0.0390.01320.28790.0736-0.05440.060.0770.2734-11.7687-19.1155-5.1334
11-0.00040.0005-0.0110.017-0.00840.08120.07680.08920.0026-0.09260.02430.072-0.0274-0.12020.09410.1020.0717-0.07060.06140.1460.2003-7.1009-26.7071-15.5568
120.00440.01870.02210.08150.10250.11890.0484-0.02250.0945-0.06980.0753-0.0643-0.09370.06910.26390.1357-0.0854-0.1015-0.0636-0.09960.25157.6631-14.7727-0.9637
130.0059-0.0009-0.00350.001-0.00030.0018-0.0566-0.00360.0322-0.00670.01590.0732-0.056-0.0405-0.00010.45670.05390.17910.8999-0.09910.52896.907-51.3096-39.6119
140.0042-0.0017-0.00440.00010.0010.0033-0.0053-0.02670.06050.0076-0.02-0.014-0.0773-0.0278-0.00010.5775-0.06320.16130.674-0.12240.451824.7353-48.4242-42.4193
150.0388-0.05730.02810.1718-0.0860.0613-0.0015-0.07720.06710.2759-0.05880.24120.0587-0.3791-0.07410.3898-0.25530.12890.7313-0.02210.156220.4956-61.5234-48.884
160.16790.1108-0.02430.08510.01060.0487-0.0596-0.1021-0.05110.1560.0036-0.14110.09830.0026-0.02070.7559-0.0762-0.24150.60970.21460.418746.8498-77.5912-32.8717
170.07610.0021-0.04330.39790.01040.03980.0051-0.124-0.20270.2439-0.1121-0.370.2624-0.0725-0.01280.4508-0.1489-0.09350.46060.09510.325744.8683-70.5154-48.8037
180.0369-0.0150.00510.0331-0.03260.02220.17950.09960.16550.07710.06760.3127-0.1145-0.2360.00590.38880.0260.03250.3449-0.02780.4468-23.7831-30.4979-7.5407
190.04140.0291-0.00630.0233-0.0037-0.0001-0.00080.03070.11590.03810.11370.08360.153-0.30270.00010.34950.00470.05080.35760.02740.3639-24.7939-28.9378-6.2382
200.03270.0180.00820.10160.10040.0822-0.02250.0359-0.0112-0.04340.1645-0.26070.27590.37910.10690.37650.1299-0.0450.40980.05080.336720.2655-41.2531-3.7619
210.02240.0132-0.00520.04120.02770.0290.0595-0.0669-0.01930.14930.0853-0.0603-0.0170.3060.04760.47020.1453-0.0310.3760.03230.254221.395-42.7946-2.9103
220.0392-0.0187-0.03290.04660.01740.02350.2878-0.03580.2242-0.03880.1526-0.2072-0.06640.0210.00020.5329-0.0704-0.03130.7132-0.03260.430141.2742-46.6359-55.2298
230.04040.0102-0.03310.0388-0.01980.02680.078-0.09530.05880.13540.1516-0.1535-0.2216-0.12890.00030.522-0.1178-0.02480.5665-0.0240.334642.8617-45.9782-54.2701
240.03880.0080.03220.0317-0.00580.02610.1759-0.1572-0.15690.01590.0110.05770.0847-0.17360.00030.9375-0.28450.04270.66480.11160.427224.8424-88.2785-48.9851
250.0152-0.0210.00720.0311-0.01940.00770.0207-0.1896-0.07730.10680.02220.04670.2063-0.04400.7008-0.27010.0820.86590.04370.401423.6203-89.1218-48.6082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 279 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 58 )
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 119 )
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 171 )
11X-RAY DIFFRACTION11chain 'B' and (resid 172 through 210 )
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 278 )
13X-RAY DIFFRACTION13chain 'C' and (resid 30 through 54 )
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 76 )
15X-RAY DIFFRACTION15chain 'C' and (resid 77 through 279 )
16X-RAY DIFFRACTION16chain 'D' and (resid 34 through 94 )
17X-RAY DIFFRACTION17chain 'D' and (resid 95 through 277 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 14 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 14 )
20X-RAY DIFFRACTION20chain 'G' and (resid 1 through 14 )
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 14 )
22X-RAY DIFFRACTION22chain 'I' and (resid 1 through 14 )
23X-RAY DIFFRACTION23chain 'J' and (resid 1 through 14 )
24X-RAY DIFFRACTION24chain 'K' and (resid 1 through 14 )
25X-RAY DIFFRACTION25chain 'L' and (resid 1 through 14 )

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