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- PDB-9c3u: Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV fr... -

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Basic information

Entry
Database: PDB / ID: 9c3u
TitleCrystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTTTAC 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
sucrose / SINEFUNGIN / DNA / DNA (> 10) / Methyltransferase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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)149,42317
Polymers147,55512
Non-polymers1,8685
Water2,810156
1
A: Methyltransferase
B: Methyltransferase
E: DNA1
F: DNA2
G: DNA1
H: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8839
Polymers73,7786
Non-polymers1,1053
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-47 kcal/mol
Surface area23850 Å2
MethodPISA
2
C: Methyltransferase
D: Methyltransferase
I: DNA1
J: DNA2
K: DNA1
L: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5408
Polymers73,7786
Non-polymers7632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-55 kcal/mol
Surface area24970 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

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DNA chain , 2 types, 8 molecules EGIKFHJL

#2: DNA chain
DNA1


Mass: 4245.776 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)
#3: DNA chain
DNA2


Mass: 4312.842 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Methyltransferase


Mass: 28330.133 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, Transferases; Transferring one-carbon groups; Methyltransferases
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 160 molecules

#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.55 %
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: 2.76→32.76 Å / Num. obs: 26041 / % possible obs: 89.4 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.9
Reflection shellResolution: 2.76→3.066 Å / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1303 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
PHENIX(1.20rc3_4406: ???)refinement
XDSJun 30, 2023 (BUILT 20230630)data reduction
Aimless0.7.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→32.76 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2741 1264 4.86 %
Rwork0.2271 --
obs0.2293 26020 65.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7463 2267 23 156 9909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510699
X-RAY DIFFRACTIONf_angle_d0.76615022
X-RAY DIFFRACTIONf_dihedral_angle_d26.2972202
X-RAY DIFFRACTIONf_chiral_restr0.0441622
X-RAY DIFFRACTIONf_plane_restr0.0071549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.880.2617117X-RAY DIFFRACTION
2.88-3.010.3375400.3292637X-RAY DIFFRACTION
3.02-3.170.3529780.29911498X-RAY DIFFRACTION36
3.17-3.370.27971080.24222619X-RAY DIFFRACTION62
3.37-3.630.28731600.23743322X-RAY DIFFRACTION80
3.63-40.28552500.23773987X-RAY DIFFRACTION97
4-4.570.25132040.20744186X-RAY DIFFRACTION100
4.57-5.760.26332150.21224167X-RAY DIFFRACTION100
5.76-6.850.2732020.22764223X-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)
10.06390.00520.0404-0.00020.00280.0314-0.0002-0.1182-0.11730.00210.16610.18450.0053-0.07140.01261.0254-0.11980.20490.44270.01620.637-17.1221-63.08396.2983
20.00480.0081-0.06740.0028-0.00620.1826-0.1426-0.3314-0.37070.11920.02950.08110.18880.0259-0.88140.22350.04920.17340.23480.33650.1574-10.2481-45.99327.7785
30.17810.049-0.08340.041-0.0270.0423-0.1213-0.0406-0.2068-0.0192-0.0161-0.15230.17640.0569-0.09660.4590.2457-0.09860.0345-0.00830.3090.6762-45.5543-1.4376
40.0099-0.03840.09390.4651-0.43380.8405-0.2210.0419-0.168-0.2854-0.03810.06440.0010.2088-0.40740.42790.06280.01420.1451-0.07120.37874.6704-45.5074-14.2246
50.1676-0.0288-0.08280.2309-0.12640.128-0.0673-0.0329-0.1558-0.17240.11980.07230.21740.0230.13180.54950.05160.2279-0.0163-0.00860.3189-12.3796-57.2595-2.7316
60.7318-0.1633-0.40610.23320.14030.2295-0.0788-0.47990.13580.27250.05760.0276-0.25930.43450.03260.3034-0.06840.04960.28-0.16620.30394.9848-21.570911.3175
70.2214-0.2044-0.2550.2890.15760.55090.0669-0.08290.361-0.29670.0539-0.216-0.19210.24590.26180.13730.1123-0.0613-0.20220.05880.17570.6098-22.7065-4.7829
80.1146-0.0324-0.0190.0753-0.00070.01220.1587-0.10770.09050.018-0.26990.0946-0.1275-0.0315-0.05830.5088-0.05950.23841.289-0.25531.09957.2193-51.488-39.2754
90.00660.00350.00720.0103-0.00950.01250.0346-0.0591-0.01290.20580.02260.0113-0.0489-0.0658-0.00010.8035-0.08660.09310.5438-0.27971.158124.8092-48.6183-42.1677
100.07-0.02120.03370.015-0.02070.04240.01260.05280.01940.0037-0.03680.02180.05930.0795-0.09750.60770.22190.24971.1367-0.3311.10822.9055-53.3387-32.0881
110.6926-0.49020.17250.4113-0.19960.10950.1226-0.21620.680.4979-0.43260.08640.0369-0.1637-0.38110.3593-0.29820.13380.7428-0.16930.479523.6373-65.6031-50.3987
120.03230.02680.0630.04570.01390.1773-0.236-0.08690.37040.0657-0.0005-0.114-0.2721-0.0482-0.00980.4368-0.15140.04841.0392-0.38310.971510.3585-52.9285-49.6388
130.05630.0159-0.11410.28380.14190.33720.0464-0.0303-0.05480.0692-0.0379-0.06780.03290.14870.1821.25350.0305-0.31080.99590.61021.292856.8929-78.4963-32.5176
140.210.06610.02710.02590.01030.0045-0.1739-0.28050.37880.4907-0.141-0.2230.0754-0.0510.00041.1562-0.3549-0.24721.10670.27350.672141.9484-77.7664-33.3273
150.4602-0.2865-0.26860.24810.0550.3478-0.19440.07590.07570.1864-0.0545-0.12580.2843-0.1222-0.74640.4184-0.3291-0.12180.30150.19620.06736.7034-69.6971-41.8143
160.1219-0.2072-0.06140.37970.06870.06030.4297-0.43960.2540.018-0.0956-0.0630.01050.21290.04720.456-0.2457-0.12750.82810.27780.663847.7254-57.4363-60.1567
170.5763-0.03290.58130.4296-0.01660.58070.46810.0294-0.1307-0.08750.08110.1220.31820.33710.19020.4722-0.13530.09050.5250.13990.434442.9793-69.9927-57.603
180.1725-0.0748-0.26520.02930.11080.4042-0.1349-0.0411-0.00530.20410.1327-0.27440.45120.1748-0.14260.7585-0.1631-0.3850.80930.33030.798951.8448-77.0217-46.2682
190.00870.02030.01310.09350.04340.0284-0.0402-0.1357-0.01690.10270.14210.03530.01670.0055-0.0221.14640.2415-0.42961.19120.06031.173554.4295-88.717-46.5974
200.05060.0559-0.06250.3510.16560.27380.0689-0.1750.54010.19880.10460.2827-0.0186-0.21660.01820.22240.0711-0.00990.5594-0.06930.4746-23.6077-30.3498-7.6327
210.411-0.01740.06270.19460.010.00580.10.29570.2195-0.22880.12430.233-0.0562-0.44190.06540.58370.16830.04180.41920.14080.4974-24.4772-28.9248-6.432
220.04590.0027-0.05960.1910.27020.4445-0.1245-0.1982-0.28140.26110.3133-0.08040.49870.64530.72090.44960.2239-0.08210.69590.09990.350820.428-41.4521-3.6919
230.06140.06520.13010.1160.05670.2533-0.0413-0.1458-0.14440.05710.1636-0.1270.23940.85290.09320.69930.3304-0.03170.6582-0.09160.211321.4678-42.8322-2.8926
240.41620.0489-0.03470.07410.05050.05340.1496-0.19210.5832-0.16550.2213-0.0803-0.06480.01470.02750.8007-0.0833-0.44830.75260.13981.384941.4832-46.6397-55.0475
250.0458-0.0585-0.04230.11960.01310.05930.4362-0.07920.13830.2230.03960.1454-0.8127-0.21270.01510.8584-0.2505-0.2251.00050.03981.109742.8083-46.1388-54.1418
260.0768-0.07830.06060.1431-0.06520.0430.3675-0.1993-0.41050.1505-0.11820.3970.329-0.281-0.00121.4484-0.34350.05810.92440.12060.708224.8879-88.3736-49.0869
270.0032-0.071-0.04110.46710.22270.11060.1005-0.4945-0.29860.13190.2604-0.02640.6372-0.09990.15140.7496-0.3937-0.00550.99670.24360.369923.8022-89.1285-48.7073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 210 )
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 278 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 119 )
7X-RAY DIFFRACTION7chain 'B' and (resid 120 through 278 )
8X-RAY DIFFRACTION8chain 'C' and (resid 30 through 54 )
9X-RAY DIFFRACTION9chain 'C' and (resid 55 through 76 )
10X-RAY DIFFRACTION10chain 'C' and (resid 77 through 92 )
11X-RAY DIFFRACTION11chain 'C' and (resid 93 through 229 )
12X-RAY DIFFRACTION12chain 'C' and (resid 230 through 279 )
13X-RAY DIFFRACTION13chain 'D' and (resid 34 through 53 )
14X-RAY DIFFRACTION14chain 'D' and (resid 54 through 94 )
15X-RAY DIFFRACTION15chain 'D' and (resid 95 through 154 )
16X-RAY DIFFRACTION16chain 'D' and (resid 155 through 186 )
17X-RAY DIFFRACTION17chain 'D' and (resid 187 through 210 )
18X-RAY DIFFRACTION18chain 'D' and (resid 211 through 264 )
19X-RAY DIFFRACTION19chain 'D' and (resid 265 through 277 )
20X-RAY DIFFRACTION20chain 'E' and (resid 1 through 14 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 14 )
22X-RAY DIFFRACTION22chain 'G' and (resid 1 through 14 )
23X-RAY DIFFRACTION23chain 'H' and (resid 1 through 14 )
24X-RAY DIFFRACTION24chain 'I' and (resid 1 through 14 )
25X-RAY DIFFRACTION25chain 'J' and (resid 1 through 14 )
26X-RAY DIFFRACTION26chain 'K' and (resid 1 through 14 )
27X-RAY DIFFRACTION27chain 'L' and (resid 1 through 14 )

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