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- PDB-8urk: Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV fr... -

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Basic information

Entry
Database: PDB / ID: 8urk
TitleCrystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrates
Components
  • DNA1
  • DNA2
  • Methyltransferase
KeywordsDNA BINDING PROTEIN / DNA N6-Adenine Methyltransferase / M.BceJIV / Burkholderia cenocepacia
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / 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: 2.11 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
DepositionOct 26, 2023Deposition 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
E: DNA1
F: DNA2
C: Methyltransferase
D: Methyltransferase
B: Methyltransferase
G: DNA1
H: DNA2
I: DNA1
J: DNA2
K: DNA1
L: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,64619
Polymers160,19712
Non-polymers2,4487
Water9,926551
1
A: Methyltransferase
E: DNA1
F: DNA2
B: Methyltransferase
G: DNA1
H: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,78411
Polymers80,0996
Non-polymers1,6865
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16190 Å2
ΔGint-26 kcal/mol
Surface area23270 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-46 kcal/mol
Surface area23730 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-732-

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, 6 molecules ACDB

#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.: 2
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 , 3 types, 556 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 50.38 %
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-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.11→97.39 Å / Num. obs: 49313 / % possible obs: 94.6 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.2
Reflection shellResolution: 2.11→2.38 Å / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2466 / CC1/2: 0.567 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX(1.20rc3_4406: ???)refinement
Aimless0.7.7data scaling
XDSJan 10, 2022 (BUILT 20220110)data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→44.27 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 2484 5.04 %
Rwork0.1839 --
obs0.1864 49285 55.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 2269 61 551 10813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610824
X-RAY DIFFRACTIONf_angle_d0.84115183
X-RAY DIFFRACTIONf_dihedral_angle_d25.9532228
X-RAY DIFFRACTIONf_chiral_restr0.0471640
X-RAY DIFFRACTIONf_plane_restr0.0061558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.150.47350.299365X-RAY DIFFRACTION1
2.15-2.20.3272100.289246X-RAY DIFFRACTION5
2.2-2.240.3286240.3025402X-RAY DIFFRACTION9
2.24-2.30.3202340.3085584X-RAY DIFFRACTION13
2.3-2.350.2672260.3083730X-RAY DIFFRACTION15
2.35-2.420.3082540.29896X-RAY DIFFRACTION19
2.42-2.490.2988490.30681145X-RAY DIFFRACTION24
2.49-2.570.3611920.30541440X-RAY DIFFRACTION31
2.57-2.660.30671040.2791817X-RAY DIFFRACTION39
2.66-2.770.31621310.2652583X-RAY DIFFRACTION55
2.77-2.890.29632110.25423942X-RAY DIFFRACTION83
2.89-3.040.29282610.23464624X-RAY DIFFRACTION99
3.04-3.230.24152450.19684692X-RAY DIFFRACTION100
3.23-3.480.22532470.16994720X-RAY DIFFRACTION100
3.48-3.830.19842580.16334689X-RAY DIFFRACTION100
3.83-4.390.19452660.13994694X-RAY DIFFRACTION100
4.39-5.530.21192270.14164773X-RAY DIFFRACTION100
5.53-44.270.23442400.1924759X-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)
10.1702-0.06390.03160.028-0.00590.0156-0.0133-0.01370.30960.2216-0.0274-0.2107-0.34660.0540.04610.6637-0.0282-0.24810.17320.18730.6131-13.4643-5.7846-50.6893
21.8946-2.21260.00192.60790.22192.2148-0.0590.0858-0.219-0.21530.00090.994-0.1158-0.40990.05390.27120.0022-0.03220.1260.0750.4824-18.728-23.1143-47.6291
30.4002-0.12640.19310.5699-0.20340.6071-0.3059-0.0150.43450.1340.10670.1709-0.6778-0.1393-0.25460.3681-0.1522-0.1123-0.26380.0450.4179-5.4048-20.1203-40.3538
41.77310.79080.21091.16670.15811.40470.094-0.0316-0.2162-0.01590.06410.44860.185-0.6316-0.13190.25220.0104-0.00540.30910.01910.4795-23.7246-38.4522-34.1555
51.4463-0.12321.02892.66051.31713.34760.0016-0.1586-0.1525-0.2382-0.01090.5402-0.3288-0.87690.08430.2952-0.01870.06760.30450.04250.4605-24.6892-39.9029-35.3888
61.13640.264-0.32820.5231-0.49780.6636-0.06940.1351-0.2069-0.42320.06580.45380.3074-0.5298-0.43510.60270.1173-0.25160.886-0.17960.50817.3781-17.7324-3.2905
70.09570.3193-0.13281.0378-0.43590.18190.17520.43550.0431-0.6216-0.21610.1060.079-0.32730.0190.45010.297-0.05570.791-0.02130.256326.4071-5.751.6525
81.2023-0.6807-0.86342.7851.35891.16710.0678-0.5190.326-0.1713-0.18940.3376-0.2231-0.0690.19820.47720.22940.00420.6928-0.08010.351220.230211.137619.4185
90.6132-0.2051-0.02040.570.16530.40980.1820.1454-0.3221-0.2944-0.23770.58340.2408-0.6863-0.06350.39210.061-0.09320.8286-0.05720.51215.07-14.643410.7227
100.25220.05690.13290.13020.42141.3658-0.05760.06060.06-0.41550.0043-0.5075-0.09650.38790.15130.82120.29170.41750.81360.35950.816253.07788.0282-6.4374
110.1856-0.04920.16080.0391-0.01960.1619-0.1923-0.02910.12360.1118-0.0316-0.1688-0.2851-0.03190.12381.0070.42790.12180.88060.36540.734137.67117.1683-6.2382
120.60810.0982-0.30940.15620.14690.4326-0.01040.09550.021-0.3206-0.0334-0.1715-0.1359-0.1448-0.03250.92780.22240.30170.89210.34530.531443.30134.8491-12.8729
130.55350.561-0.42521.17820.24051.060.20210.2383-0.1229-0.5022-0.1573-0.1781-0.2531-0.0299-0.00430.60.3460.16020.74730.15670.439841.299-1.4285-5.4217
140.2742-0.04480.09010.7749-0.08830.43380.02240.10080.0189-0.2753-0.25060.0716-0.057-0.1123-0.00620.42550.3990.09760.6240.13070.352633.30862.51674.7309
151.25170.8051-0.41011.12420.30050.69640.1747-0.01170.2408-0.0418-0.3098-0.5783-0.0430.0480.03420.32070.13490.03640.42610.06320.407247.3172-11.34619.0599
160.2166-0.229-0.24710.78580.36990.93430.04640.18510.5475-0.3542-0.1453-0.6953-0.32320.10160.03310.35680.13490.0970.53750.16130.638646.8084.654210.1122
170.9847-0.0873-0.20212.4535-0.44080.97670.17570.3120.309-0.0637-0.291-0.1709-0.42520.1799-0.02250.6690.05610.33930.5610.37631.126854.96213.54024.2592
181.06130.64690.12950.62480.39710.45130.07180.1943-0.71190.20580.0015-0.1990.46820.10280.16480.4050.01460.0350.2458-0.16690.69096.7193-60.0462-52.1514
191.64730.51111.72580.53560.53841.8238-0.09910.5499-0.31-0.19660.1168-0.1260.01460.3748-0.09510.19350.00950.01110.1457-0.12730.41455.898-44.8304-53.0628
200.5107-0.0076-0.15130.3363-0.31040.3229-0.12530.2076-0.0393-0.14450.02940.0103-0.17980.0960.02360.0885-0.1583-0.04790.0061-0.00140.30210.8848-35.8589-46.6232
210.5628-0.01320.05470.3069-0.09560.5342-0.05890.0954-0.1005-0.05550.03290.21390.1232-0.0699-0.09570.1096-0.222-0.01520.02970.06040.3395-4.0293-40.4884-44.0727
220.8360.57870.69370.53640.27820.87830.0506-0.436-0.21640.3542-0.07050.18250.1519-0.2183-0.14680.194-0.03850.14690.19160.13910.4092-14.3481-43.5233-24.1311
231.9718-0.62850.30011.97580.52740.8497-0.008-0.0722-0.0067-0.04570.1344-0.32240.19640.12320.20460.21990.01060.04420.03920.05070.26679.5545-41.9357-31.8301
240.4203-0.3226-0.24290.77410.39830.924-0.0822-0.0012-0.49120.14440.1375-0.1260.4110.20530.05150.22670.05520.01220.1201-0.03020.51217.7517-54.0782-40.6348
252.3260.454-0.66962.0702-0.20360.76910.10650.16920.35990.10180.0692-0.3974-0.72150.74320.50070.3611-0.20870.04440.35680.09240.38820.3402-27.4903-37.9549
260.25060.02260.72450.68790.16893.53-0.06460.14120.1524-0.40880.036-0.3695-0.02481.08670.15240.4235-0.21090.02190.40880.03230.331521.4581-26.0356-38.7887
271.3097-0.3843-0.8082.38440.24330.6240.46680.084-0.2862-0.04720.0632-0.2939-0.02650.325-0.43970.3890.039-0.02920.6337-0.06920.360441.3524-22.178313.6304
280.79550.22490.32421.35570.30160.7685-0.01690.4-0.2734-0.21660.0635-0.20670.5879-0.3733-0.04660.50520.15020.0460.53160.00190.311642.8283-22.808412.659
290.85930.37230.13651.4505-0.04740.17560.18470.28490.6454-0.2772-0.1340.2457-0.1535-0.57810.3950.83850.3358-0.03840.76610.16130.573224.788719.47877.3694
300.1452-0.25840.19660.755-0.80781.82070.07350.61560.14910.00150.01240.0619-0.83280.05840.00280.60830.283-0.04430.86530.06130.50623.648420.29486.977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 279 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 14 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 14 )
6X-RAY DIFFRACTION6chain 'G' and (resid 30 through 94 )
7X-RAY DIFFRACTION7chain 'G' and (resid 95 through 163 )
8X-RAY DIFFRACTION8chain 'G' and (resid 164 through 197 )
9X-RAY DIFFRACTION9chain 'G' and (resid 198 through 279 )
10X-RAY DIFFRACTION10chain 'J' and (resid 34 through 63 )
11X-RAY DIFFRACTION11chain 'J' and (resid 64 through 76 )
12X-RAY DIFFRACTION12chain 'J' and (resid 77 through 94 )
13X-RAY DIFFRACTION13chain 'J' and (resid 95 through 120 )
14X-RAY DIFFRACTION14chain 'J' and (resid 121 through 154 )
15X-RAY DIFFRACTION15chain 'J' and (resid 155 through 186 )
16X-RAY DIFFRACTION16chain 'J' and (resid 187 through 245 )
17X-RAY DIFFRACTION17chain 'J' and (resid 246 through 277 )
18X-RAY DIFFRACTION18chain 'D' and (resid 30 through 54 )
19X-RAY DIFFRACTION19chain 'D' and (resid 55 through 106 )
20X-RAY DIFFRACTION20chain 'D' and (resid 107 through 140 )
21X-RAY DIFFRACTION21chain 'D' and (resid 141 through 163 )
22X-RAY DIFFRACTION22chain 'D' and (resid 164 through 197 )
23X-RAY DIFFRACTION23chain 'D' and (resid 198 through 210 )
24X-RAY DIFFRACTION24chain 'D' and (resid 211 through 278 )
25X-RAY DIFFRACTION25chain 'E' and (resid 1 through 14 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 14 )
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 14 )
28X-RAY DIFFRACTION28chain 'I' and (resid 1 through 14 )
29X-RAY DIFFRACTION29chain 'K' and (resid 1 through 14 )
30X-RAY DIFFRACTION30chain 'L' and (resid 1 through 14 )

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