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- PDB-9c3s: Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV fr... -

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Basic information

Entry
Database: PDB / ID: 9c3s
TitleCrystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrate containing GTATAC 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: 2.16 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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)162,06517
Polymers160,19712
Non-polymers1,8685
Water5,693316
1
A: Methyltransferase
B: Methyltransferase
E: DNA1
F: DNA2
G: DNA1
H: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2049
Polymers80,0996
Non-polymers1,1053
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-43 kcal/mol
Surface area24130 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 area14100 Å2
ΔGint-42 kcal/mol
Surface area24580 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
Components on special symmetry positions
IDModelComponents
11C-417-

HOH

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Components

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DNA chain , 2 types, 8 molecules EGIKFHJL

#2: DNA chain
DNA1


Mass: 4254.791 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Burkholderia cenocepacia (bacteria)
#3: DNA chain
DNA2


Mass: 4303.829 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: 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
#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, 320 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.: 316 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
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: 2.16→32.91 Å / Num. obs: 41892 / % possible obs: 91.9 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.1
Reflection shellResolution: 2.17→2.52 Å / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2094 / CC1/2: 0.627

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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: 2.16→32.76 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 2090 4.99 %
Rwork0.189 --
obs0.1917 41883 50.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7563 2269 131 316 10279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410693
X-RAY DIFFRACTIONf_angle_d0.71715006
X-RAY DIFFRACTIONf_dihedral_angle_d25.8352195
X-RAY DIFFRACTIONf_chiral_restr0.0431621
X-RAY DIFFRACTIONf_plane_restr0.0061540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.587760.378366X-RAY DIFFRACTION
2.21-2.270.434140.3356192X-RAY DIFFRACTION
2.27-2.330.4186150.3354298X-RAY DIFFRACTION
2.33-2.40.273321456X-RAY DIFFRACTION
2.4-2.480.4047260.3366691X-RAY DIFFRACTION
2.48-2.570.3797660.3274976X-RAY DIFFRACTION
2.57-2.670.379790.31721430X-RAY DIFFRACTION27
2.67-2.790.3292960.29812059X-RAY DIFFRACTION39
2.79-2.940.30731620.27993004X-RAY DIFFRACTION58
2.94-3.120.28712480.25114514X-RAY DIFFRACTION86
3.12-3.360.24182680.19365164X-RAY DIFFRACTION98
3.36-3.70.23742650.18225213X-RAY DIFFRACTION99
3.7-4.230.21663210.15465178X-RAY DIFFRACTION99
4.23-5.330.22222350.14655280X-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)
10.2075-0.02690.00040.0796-0.00110.0981-0.0740.04040.0528-0.03590.04030.0971-0.2259-0.0688-0.26030.3233-0.02-0.15470.18910.14990.3722-16.1036-13.7991-49.1962
20.1284-0.07740.15050.1036-0.08650.2319-0.2528-0.01280.2880.14360.03210.1062-0.34430.0245-0.40480.29090.0151-0.1093-0.1280.16140.1756-5.5114-20.0039-40.3662
30.0369-0.0178-0.02360.1170.0830.06020.03670.0764-0.1867-0.0773-0.0072-0.04910.12730.09260.16050.39070.14210.05110.1987-0.11830.45495.9053-58.8704-51.6265
40.0071-0.007-0.00360.00720.00450.0026-0.13210.03980.0253-0.0727-0.0106-0.053-0.02360.05920.00010.2816-0.02640.0830.3431-0.12910.431614.5618-40.7984-50.7843
50.00720.0014-0.00780.01120.00530.01510.02950.1813-0.05130.0049-0.02110.0940.08220.1498-00.30560.0568-0.00750.4049-0.05020.26084.2563-44.9252-58.9198
60.03390.02470.12070.0390.03210.6073-0.0390.1115-0.06760.04560.01240.0177-0.14370.1717-0.04880.1407-0.0113-0.00580.0932-0.02160.1991-0.0838-38.915-47.0898
70.14480.03150.01720.15440.12670.102-0.01160.0073-0.07210.0623-0.00590.0820.0760.02560.00290.1791-0.10120.05920.11180.05280.26-5.4712-42.2684-39.5998
80.0436-0.01520.10140.0201-0.04090.23310.0978-0.1504-0.08950.0982-0.03830.00340.0872-0.115-0.07720.2143-0.02880.15020.06420.12370.1648-7.0178-42.1954-26.0871
90.03630.01730.01910.1440.1690.1977-0.00850.0258-0.2150.16350.0506-0.03680.15660.06180.0660.23640.03720.08490.024-0.05270.3497.7473-54.1114-40.6867
100.00650.0059-0.00280.0088-0.00180.0010.06390.0733-0.11850.09650.11330.08420.0806-0.19810.00020.45420.0804-0.17021.2123-0.15470.6188.0863-17.7286-4.7278
110.01420.01160.01170.01020.00940.00860.0537-0.0138-0.2077-0.078-0.09850.02930.017-0.196800.43780.0881-0.11070.978-0.12610.453224.3015-18.7325-3.5611
120.20030.0174-0.1420.11520.07780.62820.08720.169-0.0311-0.1189-0.08120.00080.0261-0.03080.03290.35330.2511-0.0040.675-0.01040.173227.4884-7.40421.3136
130.01510.0312-0.01010.0649-0.02120.0068-0.04340.11720.13650.09950.14460.14780.022-0.1292-0.00360.52360.3043-0.03991.1754-0.04870.355814.46615.07399.0341
140.00430.00290.00540.0040.00260.00640.0679-0.09120.1230.0643-0.0110.02630.01950.00180.00010.68360.246-0.05890.9671-0.06610.512822.827215.826623.5096
150.44740.0350.0040.10750.04560.12070.0423-0.0846-0.0812-0.0941-0.14890.0743-0.1896-0.3181-0.14540.33640.2326-0.02360.7939-0.02120.276820.8322-6.957714.6864
160.00680.0047-0.00220.00690.0020.0032-0.08930.0602-0.0914-0.0440.01150.1008-0.0636-0.140200.44160.1373-0.1231.1577-0.05770.571310.1101-11.77227.0448
170.49450.0385-0.17940.022-0.03410.0867-0.12490.0758-0.0297-0.0696-0.0390.0198-0.1132-0.069-0.03460.486-0.0035-0.12641.0516-0.02040.358810.2118-20.51639.3381
18-0.00020-0.00060.0004-0.00210.0056-0.13740.10640.0937-0.11770.05740.0367-0.09080.1636-0.00020.89150.04140.2220.80680.22170.785956.04047.8594-10.6568
190.52550.14770.20080.16130.11730.1078-0.23740.04830.0127-0.31710.0355-0.1129-0.249-0.2168-0.19860.90360.20320.13880.67290.26060.394541.56228.8839-8.6869
200.11770.12360.03640.12980.03790.01170.06510.018-0.0663-0.0203-0.0372-0.053-0.01760.05590.02710.63920.20190.10010.71250.14180.289641.0752-1.6166-5.7137
210.21730.0288-0.13810.10510.16130.4024-0.10210.01450.1207-0.0022-0.0863-0.0367-0.1659-0.0885-0.2410.51870.2626-0.03690.60890.11430.299133.99362.77355.8174
220.08980.1873-0.0080.3832-0.01710.0014-0.04530.1577-0.0864-0.1518-0.116-0.1006-0.2348-0.2584-0.04920.35980.19780.08950.610.07120.294242.3738-3.81657.0907
230.00590.00210.00090.00370.0010.0047-0.0153-0.008-0.0404-0.01170.0435-0.0486-0.0161-0.0301-00.4740.07610.04510.49630.01430.344843.1193-14.673528.5306
240.00180.0130.01680.04350.05750.0717-0.0814-0.06770.2629-0.0524-0.0006-0.2966-0.36950.14620.01170.49450.0894-0.02610.50840.06840.477347.92674.65159.6373
250.00030.0022-0.00310.0075-0.00980.00980.0290.05020.0213-0.00180.0647-0.1703-0.07030.11860.00010.7345-0.04720.19160.53070.12740.620154.747115.32611.8106
260.19220.1388-0.03370.4109-0.11760.49150.1658-0.1658-0.2709-0.08220.17120.46010.2437-0.50250.29240.3035-0.0082-0.02440.36020.00650.4784-23.7447-38.4253-34.1323
270.1129-0.095-0.0060.106-0.01850.0289-0.097-0.1431-0.1269-0.38970.11690.1141-0.2831-0.58140.00020.375-0.0337-0.04230.3470.03240.3661-24.6357-39.8879-35.3584
280.0267-0.084-0.00980.3618-0.02470.0877-0.03530.16170.12580.00760.0589-0.3218-0.40250.44840.37130.3244-0.12950.05710.42820.11310.365220.3943-27.4616-37.8933
290.1767-0.00090.13480.05470.04350.1383-0.01950.1319-0.031-0.10330.097-0.04010.01390.57850.03190.4641-0.19020.04280.51880.02150.273821.4598-26.0864-38.6773
300.0730.04610.0490.12140.00430.03770.26950.0252-0.24050.22210.2723-0.27620.1487-0.04310.0040.5710.1442-0.00250.7029-0.0370.497441.3242-22.263913.468
310.08950.07320.06670.10820.03840.0507-0.00120.1174-0.0017-0.16270.0754-0.05990.3914-0.288900.62820.10260.02960.72680.02320.333642.8561-22.852712.6005
320.13140.0366-0.09610.0121-0.02660.17330.02150.03120.1818-0.05970.12540.1585-0.1093-0.23630.34310.99480.4293-0.08590.72930.08620.528824.72519.45997.3752
330.2453-0.3162-0.26280.41160.34060.28360.15190.2004-0.1687-0.05190.16470.1771-0.2067-0.0170.14480.68840.3618-0.13190.85360.06360.43223.642320.28926.9693
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 279 )
3X-RAY DIFFRACTION3chain 'B' and (resid 30 through 58 )
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 140 )
7X-RAY DIFFRACTION7chain 'B' and (resid 141 through 171 )
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 210 )
9X-RAY DIFFRACTION9chain 'B' and (resid 211 through 278 )
10X-RAY DIFFRACTION10chain 'C' and (resid 36 through 54 )
11X-RAY DIFFRACTION11chain 'C' and (resid 55 through 90 )
12X-RAY DIFFRACTION12chain 'C' and (resid 91 through 154 )
13X-RAY DIFFRACTION13chain 'C' and (resid 155 through 171 )
14X-RAY DIFFRACTION14chain 'C' and (resid 172 through 186 )
15X-RAY DIFFRACTION15chain 'C' and (resid 187 through 230 )
16X-RAY DIFFRACTION16chain 'C' and (resid 231 through 254 )
17X-RAY DIFFRACTION17chain 'C' and (resid 255 through 279 )
18X-RAY DIFFRACTION18chain 'D' and (resid 37 through 54 )
19X-RAY DIFFRACTION19chain 'D' and (resid 55 through 94 )
20X-RAY DIFFRACTION20chain 'D' and (resid 95 through 120 )
21X-RAY DIFFRACTION21chain 'D' and (resid 121 through 140 )
22X-RAY DIFFRACTION22chain 'D' and (resid 141 through 171 )
23X-RAY DIFFRACTION23chain 'D' and (resid 172 through 186 )
24X-RAY DIFFRACTION24chain 'D' and (resid 187 through 254 )
25X-RAY DIFFRACTION25chain 'D' and (resid 255 through 277 )
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 14 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 14 )
28X-RAY DIFFRACTION28chain 'G' and (resid 1 through 14 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 14 )
30X-RAY DIFFRACTION30chain 'I' and (resid 1 through 14 )
31X-RAY DIFFRACTION31chain 'J' and (resid 1 through 14 )
32X-RAY DIFFRACTION32chain 'K' and (resid 1 through 14 )
33X-RAY DIFFRACTION33chain 'L' and (resid 1 through 14 )

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