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- PDB-7vru: Crystal structure of PacII_M1M2S-DNA-SAH complex -

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Basic information

Entry
Database: PDB / ID: 7vru
TitleCrystal structure of PacII_M1M2S-DNA-SAH complex
Components
  • (DNA (25-mer)) x 2
  • (Site-specific DNA-methyltransferase (adenine- ...) x 2
  • Site-specific DNA recognition subunit
KeywordsTRANSFERASE/DNA / Type I R-M system PacII methytransferase m4C and m6A modification complex / BIOSYNTHETIC PROTEIN / TRANSFERASE-DNA complex
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA binding
Similarity search - Function
DNA methylase specificity domains / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal 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 ...DNA methylase specificity domains / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Site-specific DNA-methyltransferase (adenine-specific) / Site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesPseudomonas alcaligenes (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZhu, J. / Gao, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31922037 China
Citation
Journal: Nat Commun / Year: 2022
Title: Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems.
Authors: Zhu, J. / Gao, Y. / Wang, Y. / Zhan, Q. / Feng, H. / Luo, X. / Li, P. / Liu, S. / Hou, H. / Gao, P.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Structural basis underlying complex assembly and conformational transition of the type I R-M system
Authors: Yanping, L. / Xiaoxue, Y.
History
DepositionOct 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Site-specific DNA-methyltransferase (adenine-specific)
C: Site-specific DNA recognition subunit
H: DNA (25-mer)
I: DNA (25-mer)
A: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,3307
Polymers173,5615
Non-polymers7692
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the complex generate a peak at 12 mL in superdex G200 16/60 column (GE Healthcare)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19540 Å2
ΔGint-109 kcal/mol
Surface area58860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.800, 122.655, 131.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Site-specific DNA-methyltransferase (adenine- ... , 2 types, 2 molecules BA

#1: Protein Site-specific DNA-methyltransferase (adenine-specific)


Mass: 58123.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas alcaligenes (bacteria) / Gene: A0T30_13470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142ISP2
#5: Protein Site-specific DNA-methyltransferase (adenine-specific)


Mass: 56900.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas alcaligenes (bacteria) / Gene: A0T30_13480 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142ISP4, site-specific DNA-methyltransferase (adenine-specific)

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Protein , 1 types, 1 molecules C

#2: Protein Site-specific DNA recognition subunit


Mass: 43180.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas alcaligenes (bacteria) / Gene: pacIIS / Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules HI

#3: DNA chain DNA (25-mer) / ssDNA_F


Mass: 7620.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (25-mer) / ssDNA_R


Mass: 7735.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 285 molecules

#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 51.8 % / Description: biconical
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Imidazole (pH 6.7-7.2), 37%-40% PEG 400 / PH range: 6.7-7.2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→41.24 Å / Num. obs: 69399 / % possible obs: 99.29 % / Redundancy: 2 % / Biso Wilson estimate: 51.6 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03114 / Rpim(I) all: 0.03114 / Rrim(I) all: 0.04404 / Net I/σ(I): 17.54
Reflection shellResolution: 2.402→2.488 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2469 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 6698 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.2469 / Rrim(I) all: 0.3492 / % possible all: 97.19

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
Coot0.9.2model building
RefinementMethod to determine structure: SAD / Resolution: 2.4→41.24 Å / SU ML: 0.2987 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 3504 5.07 %
Rwork0.1899 65591 -
obs0.1922 69095 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10792 1025 52 283 12152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008412234
X-RAY DIFFRACTIONf_angle_d0.993316761
X-RAY DIFFRACTIONf_chiral_restr0.0541838
X-RAY DIFFRACTIONf_plane_restr0.00851989
X-RAY DIFFRACTIONf_dihedral_angle_d18.64881987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.32011290.25322426X-RAY DIFFRACTION92.47
2.43-2.470.30791270.24622602X-RAY DIFFRACTION99.67
2.47-2.510.28851340.24282624X-RAY DIFFRACTION99.35
2.51-2.550.3221350.24232582X-RAY DIFFRACTION99.45
2.55-2.590.27891510.23872594X-RAY DIFFRACTION99.28
2.59-2.630.33651310.2362621X-RAY DIFFRACTION99.28
2.63-2.680.28261430.23212615X-RAY DIFFRACTION99.82
2.68-2.730.30611320.22382612X-RAY DIFFRACTION99.71
2.73-2.790.2861500.22552595X-RAY DIFFRACTION99.49
2.79-2.850.26281290.22852639X-RAY DIFFRACTION99.57
2.85-2.910.29971340.23732614X-RAY DIFFRACTION99.71
2.91-2.990.31481560.24462636X-RAY DIFFRACTION99.75
2.99-3.070.30021350.23922594X-RAY DIFFRACTION99.67
3.07-3.160.29721460.22942635X-RAY DIFFRACTION99.57
3.16-3.260.28911380.21852615X-RAY DIFFRACTION99.85
3.26-3.380.26511450.21722640X-RAY DIFFRACTION99.86
3.38-3.510.29011380.21522665X-RAY DIFFRACTION99.79
3.51-3.670.21211290.19432647X-RAY DIFFRACTION99.78
3.67-3.860.23911460.17972639X-RAY DIFFRACTION99.86
3.86-4.110.20811370.16932667X-RAY DIFFRACTION99.82
4.11-4.420.21721320.15522673X-RAY DIFFRACTION99.82
4.42-4.870.16551780.15232649X-RAY DIFFRACTION99.79
4.87-5.570.2031450.15662678X-RAY DIFFRACTION99.44
5.57-7.010.21291370.18092706X-RAY DIFFRACTION99.06
7.01-41.240.17431470.14862623X-RAY DIFFRACTION92.03
Refinement TLS params.Method: refined / Origin x: 10.0915685179 Å / Origin y: 69.8399108756 Å / Origin z: 91.2792063254 Å
111213212223313233
T0.303133467154 Å2-0.0375502931503 Å2-0.00885478000869 Å2-0.306547275493 Å2-0.0201503878056 Å2--0.33281935419 Å2
L0.256969288122 °2-0.106441515757 °2-0.0690702455746 °2-0.541151073791 °2-0.181962405694 °2--0.536543359955 °2
S0.0107551703604 Å °-0.0237681599188 Å °0.0107389394999 Å °0.0333835901797 Å °0.0485561104299 Å °0.128174427868 Å °0.0725741066758 Å °0.0203418582793 Å °1.32881862541E-5 Å °
Refinement TLS groupSelection details: all

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