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- PDB-7qw7: Adenine-specific DNA methyltransferase M.BseCI complexed with Ado... -

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Basic information

Entry
Database: PDB / ID: 7qw7
TitleAdenine-specific DNA methyltransferase M.BseCI complexed with AdoHcy and cognate fully methylated DNA duplex
Components
  • (Fully methylated DNA duplex) x 2
  • Modification methylase BseCI
KeywordsTRANSFERASE / Methyltransferase / DNA-modification / Adenine-N6 methylation / Base flipping
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / 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
S-ADENOSYL-L-HOMOCYSTEINE / DNA / Type II methyltransferase M.BseCI
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMitsikas, D.A. / Kouyianou, K. / Kotsifaki, D. / Providaki, M. / Bouriotis, V. / Glykos, N.M. / Kokkinidis, M.
Funding support Greece, 1items
OrganizationGrant numberCountry
Not funded Greece
CitationJournal: To Be Published
Title: Structure of M.BseCI DNA methyltransferase from Geobacillus stearothermophilus.
Authors: Mitsikas, D.A. / Kouyianou, K. / Kotsifaki, D. / Providaki, M. / Bouriotis, V. / Glykos, N.M. / Kokkinidis, M.
History
DepositionJan 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Modification methylase BseCI
Z: Fully methylated DNA duplex
Y: Fully methylated DNA duplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2644
Polymers73,8793
Non-polymers3841
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-15 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.010, 88.010, 155.481
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Modification methylase BseCI / M.BseCI / Adenine-specific methyltransferase BseCI


Mass: 67761.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: bseCIM / Production host: Escherichia coli (E. coli)
References: UniProt: P43423, site-specific DNA-methyltransferase (adenine-specific)
#2: DNA chain Fully methylated DNA duplex


Mass: 3059.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#3: DNA chain Fully methylated DNA duplex


Mass: 3059.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: Glycerol ethoxylate, Tris-HCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.6→44.01 Å / Num. obs: 19732 / % possible obs: 94.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 72.05 Å2 / CC1/2: 0.927 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Rrim(I) all: 0.13 / Χ2: 0.68 / Net I/σ(I): 5.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.317 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2101 / CC1/2: 0.189 / Rpim(I) all: 1.325 / Rrim(I) all: 2.683 / Χ2: 0.81 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QW5

7qw5


Resolution: 2.6→44.01 Å / SU ML: 0.4861 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 973 4.95 %Random selection
Rwork0.1981 18677 --
obs0.1991 19650 93.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.9 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 74.63 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 402 26 47 4947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845048
X-RAY DIFFRACTIONf_angle_d0.89366902
X-RAY DIFFRACTIONf_chiral_restr0.0525755
X-RAY DIFFRACTIONf_plane_restr0.0037814
X-RAY DIFFRACTIONf_dihedral_angle_d14.55261920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.45541210.40782341X-RAY DIFFRACTION82.34
2.74-2.910.3441460.31972799X-RAY DIFFRACTION98.86
2.91-3.130.3111450.28332827X-RAY DIFFRACTION99.13
3.13-3.440.29031460.25672724X-RAY DIFFRACTION99.38
3.47-3.950.19141180.19312280X-RAY DIFFRACTION84.92
3.95-4.970.16561530.15712834X-RAY DIFFRACTION99.6
4.97-44.010.18681440.162872X-RAY DIFFRACTION99.57
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)
13.345119520480.157471349730.9803954330781.909149045650.5119422429783.667929018160.215518494494-0.67590320815-0.156615176461-0.133614549621-0.3543491595240.198042466614-0.283379423627-1.014637265750.298416238310.181533308503-0.02315271086970.03009312546430.423405342699-0.01762171666790.25742715313258.264849664657.517150284314.0517835949
20.209158417518-0.50264251067-0.3937060179713.17487313373-0.1617860585711.44188704472-0.1022707038310.188810271283-0.3697953411780.7893838816450.2396104678450.285884015579-0.269421831650.2606260952360.9432190374070.546577948433-0.128939023822-0.01723235638860.616370488433-0.071452542610.37159317217756.510108859456.946823157516.4151263755
31.89660837770.819266379201-0.5448255462572.918080858180.1632363902612.06140553420.0163160985128-0.01254002659180.168716909366-0.07153089240770.04820729905010.0924304806884-0.303318939889-0.08345626696981.59065201111E-80.642058744008-0.01687441105490.002987136577920.5569663852920.006364731294450.5860706778572.770282293175.77215520062.67443921234
41.9602582612-0.007238670110460.4293747976262.72803975285-0.4836702980822.00754595281-0.0570607847028-0.0908497753783-0.2558879355750.07024743875560.152639894647-0.4382911000850.1483997979510.3178653285688.79870606988E-80.5789732947750.03212540698970.002786391187660.542250978732-0.06400357439110.63422719672180.789246106957.79924159386.03666777243
52.318518727220.0734901879987-0.2333026084491.918406020110.192076217091.439545646580.109820561815-0.299192647938-0.04991578831180.234981590229-0.1114460119740.1434677564550.412228989821-0.17876812790.000108562135930.616392351915-0.1087286833770.0313408184490.5292114165810.0366339674680.50333775227253.099281672143.29668118716.9332568312
60.490411110191-0.3568353714690.127955606550.413071890818-0.3172010617730.3793720463950.144728419471-0.115865775191-0.3480093845960.418806126077-0.368418605067-0.0977513515950.7598739558710.0389583626625-0.00256650044751.06812415056-0.035017405842-0.02273868777660.5489964221760.158541819110.74901467629371.142846288125.490988883918.6376755267
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'Z' and (resid 1 through 10 )ZD1 - 10
22chain 'Y' and (resid 11 through 20 )YD11 - 20
33chain 'A' and (resid 9 through 192 )AA9 - 1921 - 172
44chain 'A' and (resid 193 through 309 )AA193 - 309173 - 286
55chain 'A' and (resid 310 through 534 )AA310 - 534287 - 511
66chain 'A' and (resid 535 through 576 )AA535 - 576512 - 553

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