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- PDB-7qw5: Adenine-specific DNA methyltransferase M.BseCI complexed with Ado... -

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Basic information

Entry
Database: PDB / ID: 7qw5
TitleAdenine-specific DNA methyltransferase M.BseCI complexed with AdoHcy and cognate unmethylated DNA duplex
Components
  • (Unmethylated DNA duplex) x 2
  • Modification methylase BseCI
KeywordsTRANSFERASE / Methyltransferase / DNA-modification / Adenine-N6 methylation / Base flipping
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification 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
S-ADENOSYL-L-HOMOCYSTEINE / DNA / Type II methyltransferase M.BseCI
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,2364
Polymers73,8513
Non-polymers3841
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-26 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.040, 87.040, 156.350
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 Unmethylated DNA duplex


Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#3: DNA chain Unmethylated DNA duplex


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#4: Chemical ChemComp-SAH / 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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 400, Tris-HCl, KCl, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.91 Å / Num. obs: 38301 / % possible obs: 99.5 % / Redundancy: 1 % / Biso Wilson estimate: 53.09 Å2 / Rsym value: 0.059 / Net I/σ(I): 22.8
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3358 / Rsym value: 0.489 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
CRANKphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→28.49 Å / SU ML: 0.3151 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.4985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1466 4.99 %Random selection
Rwork0.1972 27884 --
obs0.1986 31905 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.7 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 70.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 400 26 243 5046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354947
X-RAY DIFFRACTIONf_angle_d0.73086767
X-RAY DIFFRACTIONf_chiral_restr0.0576745
X-RAY DIFFRACTIONf_plane_restr0.0031797
X-RAY DIFFRACTIONf_dihedral_angle_d15.36921882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.34121270.30092795X-RAY DIFFRACTION98.95
2.38-2.480.29871400.29342792X-RAY DIFFRACTION98.55
2.48-2.590.27961530.28012767X-RAY DIFFRACTION99.12
2.59-2.730.31251570.2892769X-RAY DIFFRACTION98.65
2.73-2.90.3451380.27482819X-RAY DIFFRACTION98.7
2.9-3.120.3161430.26432769X-RAY DIFFRACTION98.81
3.12-3.430.29541350.23742811X-RAY DIFFRACTION98.83
3.43-3.930.21131520.18262777X-RAY DIFFRACTION98.89
3.93-4.950.15591550.14282780X-RAY DIFFRACTION98.52
4.95-28.490.18051660.15142805X-RAY DIFFRACTION98.28
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)
11.151953225291.01426236767-0.2713341379832.243784854840.2207846552312.24590585206-0.126134165592-0.01939279848890.220872868856-0.2502296607450.202923366754-0.364114172144-0.7985958078480.2086704715870.06805056658610.842583085526-0.0794883227488-0.02178194683810.379117267986-0.0146615989270.56163578237276.380249216679.23293201943.75858291113
20.916312959121.03945913639-0.01016935831191.821390373760.4614512710211.30768670232-0.1581175769130.00421497401910.0815589511287-0.383862853330.176687830520.00575557971962-0.344265576812-0.0624196814560.01973232402960.538745409491-0.041822496701-0.06863324277940.346133426229-0.02536974224580.42873844632568.250437327764.47360895151.3385972681
30.5566253600250.07860200079160.438831264892.139871446210.07283994529881.06423360209-0.02510609857790.0510361231371-0.288976240072-0.03209157291370.00252270445574-0.6716104963430.1813653031250.596844107643-0.02247458434790.585032487078-0.0145647923872-0.07933790779310.622746295496-0.0862743030280.76940387182286.335358645255.938391574810.7970402083
40.750263714110.794646002150.3546723924941.35734575265-0.06635047322191.29130159348-0.0271310462932-0.199329871798-0.04301154230610.2295359149950.028926926133-0.1338938807220.379278119536-0.0254334686318-5.28747064814E-90.648254228448-0.0555907509245-0.01548525933380.503866401249-0.02184429594160.55282028084561.929940220446.006825170513.842003681
50.6762891360590.7534818856-0.3661744331141.344420265880.1932451027950.9006122092610.184622596347-0.0510278132926-0.270629032940.709261513879-0.3465702171580.2014246434530.465647985875-0.250466999561-0.01069444217630.672715608542-0.2711424242210.1408549353550.729480047882-0.04551273802570.49917532274843.187092199241.602387617821.0858187876
62.01253128986-0.0422603836958-0.5505734456732.044084539760.3325051987311.550735112780.185762585595-0.288289218581-0.01657683427550.282451323613-0.2482560581120.4565132136940.303420351618-0.6555786296430.002065826923940.593733728465-0.1846684060590.09263930840980.696673974456-0.01966261227740.49825638038145.385454973345.720378603618.2455817163
71.284315753970.0677883269081-0.3193824698540.5497587746690.3307367470740.9548043024590.0594413630703-0.165972981142-0.5804579814520.299849224748-0.0367301772795-0.262503842490.6746296605570.1483806954690.0005218180443720.852495053638-0.0168027395484-0.09739811117950.4175192716510.09719168585010.68292025118268.675666977833.501558634114.4721041441
81.635382775810.6869909683620.1032381277981.755224171731.156149321880.8492149002060.292163648348-0.5289233907680.1648376767340.164269948243-0.438770369938-0.146031497369-0.0368872641099-0.713952630230.1138620568860.551458848515-0.102241674486-0.02900320609020.593968928272-0.02143465120730.36129853881857.6592995557.138754925113.9205461879
91.154633384790.12776674752-0.3050684077340.795576471633-0.1731141998870.1049155300260.2086673824390.0504351228347-0.0690283654480.22258307966-0.1133562349340.524154234517-0.2430393000920.05005016475260.08567966360410.674108065472-0.1240895450940.04791723254480.629087310755-0.08762349013440.46961728064255.887969895256.745082171516.3866550217
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 138 )AA10 - 1381 - 115
22chain 'A' and (resid 139 through 232 )AA139 - 232116 - 209
33chain 'A' and (resid 233 through 281 )AA233 - 281210 - 253
44chain 'A' and (resid 282 through 372 )AA282 - 372254 - 344
55chain 'A' and (resid 373 through 402 )AA373 - 402345 - 372
66chain 'A' and (resid 403 through 486 )AA403 - 486373 - 456
77chain 'A' and (resid 487 through 576 )AA487 - 576457 - 544
88chain 'Z' and (resid 1 through 10 )ZB1 - 10
99chain 'Y' and (resid 11 through 20 )Y - ZYB11 - 20

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