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- PDB-7qw8: Adenine-specific DNA methyltransferase M.BseCI -

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Basic information

Entry
Database: PDB / ID: 7qw8
TitleAdenine-specific DNA methyltransferase M.BseCI
ComponentsModification 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
Type II methyltransferase M.BseCI
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: Modification methylase BseCI
B: Modification methylase BseCI


Theoretical massNumber of molelcules
Total (without water)135,5222
Polymers135,5222
Non-polymers00
Water3,873215
1
A: Modification methylase BseCI


Theoretical massNumber of molelcules
Total (without water)67,7611
Polymers67,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Modification methylase BseCI


Theoretical massNumber of molelcules
Total (without water)67,7611
Polymers67,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.700, 85.700, 151.800
Angle α, β, γ (deg.)90.000, 95.100, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 80 or (resid 81...
d_2ens_1(chain "B" and (resid 23 through 37 or (resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPASPA1 - 178
d_12ens_1LYSSERA180 - 523
d_21ens_1ASPVALB4 - 91
d_22ens_1GLULYSB94 - 128
d_23ens_1ASPASPB132 - 186
d_24ens_1LYSPHEB188 - 190
d_25ens_1VALASNB192 - 203
d_26ens_1ASNASPB206 - 218
d_27ens_1SERSERB221 - 536

NCS oper: (Code: givenMatrix: (0.999959567523, 0.00141881611991, -0.0088797679987), (0.00179619653349, -0.999089045779, 0.0426362789546), (-0.00881118589669, -0.0426505048728, -0.999051198607)Vector: ...NCS oper: (Code: given
Matrix: (0.999959567523, 0.00141881611991, -0.0088797679987), (0.00179619653349, -0.999089045779, 0.0426362789546), (-0.00881118589669, -0.0426505048728, -0.999051198607)
Vector: 21.0871097449, 28.5747428035, 226.819973748)

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Components

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


Mass: 67761.094 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 290 K / Method: microdialysis / pH: 6.6 / Details: PEG, MES, ammonium sulfate

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Data collection

DiffractionMean temperature: 283 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 4, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 2.5→24.71 Å / Num. obs: 46250 / % possible obs: 97.3 % / Redundancy: 5 % / Biso Wilson estimate: 46.61 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4485 / % possible all: 94.2

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Processing

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

7qw5


Resolution: 2.5→24.71 Å / SU ML: 0.2721 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 2343 5.07 %Random selection
Rwork0.1696 43901 --
obs0.1714 46244 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.8 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 61.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8449 0 0 215 8664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328630
X-RAY DIFFRACTIONf_angle_d0.697111670
X-RAY DIFFRACTIONf_chiral_restr0.05531299
X-RAY DIFFRACTIONf_plane_restr0.00371492
X-RAY DIFFRACTIONf_dihedral_angle_d10.63823209
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.813933024697 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.31811390.22562494X-RAY DIFFRACTION93.44
2.55-2.610.26941240.22542527X-RAY DIFFRACTION95.46
2.61-2.670.24361460.21532488X-RAY DIFFRACTION94.11
2.67-2.730.29841350.21332523X-RAY DIFFRACTION96.27
2.73-2.810.25191600.19922547X-RAY DIFFRACTION96.58
2.81-2.890.23221670.19542500X-RAY DIFFRACTION96.91
2.89-2.980.21061300.18262575X-RAY DIFFRACTION95.68
2.98-3.090.24641350.20012586X-RAY DIFFRACTION98.52
3.09-3.210.25231110.19242563X-RAY DIFFRACTION96.57
3.21-3.360.24531560.18062612X-RAY DIFFRACTION97.16
3.36-3.540.21291220.16882596X-RAY DIFFRACTION98.76
3.54-3.760.17151230.16012639X-RAY DIFFRACTION98.64
3.76-4.050.18721420.15632641X-RAY DIFFRACTION98.72
4.05-4.450.15811410.13912638X-RAY DIFFRACTION98.86
4.45-5.090.16151200.13892651X-RAY DIFFRACTION98.79
5.09-6.390.20411350.17572668X-RAY DIFFRACTION99.4
6.39-24.710.20221570.15872653X-RAY DIFFRACTION97.06
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)
11.58155052283-0.117697118371-0.219327141890.73367671676-0.536862063761.12646148538-0.299714782004-0.4875407988590.1145069188420.3697873329660.02471722151-0.282105240072-0.522061022810.615702890451-0.6297540687720.734775086472-0.0750078654861-0.2399217579650.863788666475-0.03463477712880.4255427986984.5279143088238.4523757998111.235178229
22.69837454287-1.062458832070.2437074609560.5408678167370.33754998421.558663880420.0282767234622-0.1023371278470.3478389919880.0798969150706-0.0955728610201-0.0210645163824-0.2955293630820.0752631039184-9.07631600773E-80.496414311814-0.0499909102166-0.0445442142840.3802352588640.0221076750290.389925586357-7.6608509789240.9996859295.1395430507
30.675337041711-0.615919484816-0.139088686523.436925156220.63065276390.5460572314160.013132965861-0.0542563230477-0.01318450797290.1984350332780.00396411255724-0.1790214890430.0538282281427-0.0001259534708360.0002714642771070.3107645432350.00704861318992-0.04388385554730.366402909312-0.001241871996340.363110129143-19.93980198650.88726055166383.6738266462
41.26981013595-0.322990171135-0.02178259165351.12132081603-0.046807679561.440871158590.04082057759670.09215871499880.0955699628103-0.0353369451588-0.00556279607928-0.0421169358638-0.0825122899779-0.0325433569555-2.31977074374E-70.2981319576910.01176195248620.01186896811780.2919081327220.01262215608420.339252618622-29.915923614522.721803240681.3656666993
52.019173829760.218592289872-0.6233853582581.40026950308-0.3145527435073.64751498991-0.1350514440860.0560315803787-0.114648405015-0.00458332884972-0.09069263028220.02637392526390.3866203308820.366398535991-0.002753581773130.4802019904690.0872685651130.05136801576080.4092236111450.007453233810490.34290249081919.929428635-6.47495461145120.214644675
61.214039526190.54997050489-0.0481981813023.200904789080.7265994811910.618347763097-0.002160652567360.06118313747070.0361506149385-0.222711875060.0501770948787-0.0859104989318-0.03148923971120.02457177208090.0009132258166410.2695500102760.01681563088740.01516678449240.3491768342680.02145771521450.29828951579-3.0827550407623.8448299034143.867331756
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 191 )AA23 - 1911 - 154
22chain 'A' and (resid 192 through 309 )AA192 - 309155 - 256
33chain 'A' and (resid 310 through 484 )AA310 - 484257 - 431
44chain 'A' and (resid 485 through 578 )AA485 - 578432 - 525
55chain 'B' and (resid 20 through 309 )BB20 - 3091 - 269
66chain 'B' and (resid 310 through 576 )BB310 - 576270 - 536

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