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- PDB-7vs4: Crystal structure of PacII_M1M2S-DNA(m6A)-SAH complex -

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Basic information

Entry
Database: PDB / ID: 7vs4
TitleCrystal structure of PacII_M1M2S-DNA(m6A)-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
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
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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhu, J. / Gao, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31922037 China
National Natural Science Foundation of China (NSFC)32130057 China
National Natural Science Foundation of China (NSFC)81921005 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 1.1Nov 29, 2023Group: 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: Site-specific DNA-methyltransferase (adenine-specific)
B: Site-specific DNA-methyltransferase (adenine-specific)
C: Site-specific DNA recognition subunit
H: DNA (25-mer)
I: DNA (25-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,1717
Polymers172,4035
Non-polymers7692
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SDS-PAGE and superdex G200 16/60 column (GE Healthcare) provide evidence
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20150 Å2
ΔGint-101 kcal/mol
Surface area57850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.095, 121.668, 129.753
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 AB

#1: Protein Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase / M1


Mass: 56572.133 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) / Strain (production host): DE3
References: UniProt: A0A142ISP4, site-specific DNA-methyltransferase (adenine-specific)
#2: Protein Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase


Mass: 57607.355 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) / Strain (production host): DE3
References: UniProt: A0A142ISP2, site-specific DNA-methyltransferase (adenine-specific)

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Protein , 1 types, 1 molecules C

#3: Protein Site-specific DNA recognition subunit


Mass: 42852.215 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) / Strain (production host): DE3

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DNA chain , 2 types, 2 molecules HI

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


Mass: 7620.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (25-mer) / ssDNA(m6A)_R


Mass: 7750.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 421 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.73 Å3/Da / Density % sol: 55 % / Description: biconical or anomaly cylindrical object
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15 M di-ammonium hydrogen phosphate, 25% PEG 3350, 0.2M Li2SO4, 0.1 M Tris pH 8.5, 20% PEG 3350 (another condition)
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: 0.979 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→49.17 Å / Num. obs: 56313 / % possible obs: 98.84 % / Redundancy: 1.6 % / Biso Wilson estimate: 35.96 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.02371 / Rpim(I) all: 0.02317 / Rrim(I) all: 0.03277 / Net I/σ(I): 18.54
Reflection shellResolution: 2.55→2.641 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 5361 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.319 / Rrim(I) all: 0.4352

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000v1.0data reduction
PHENIX1.19.2_4158phasing
Coot0.9.2model building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VRU

7vru


Resolution: 2.55→49.17 Å / SU ML: 0.2978 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 2766 4.94 %
Rwork0.1808 53239 -
obs0.1835 56005 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.24 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10789 1026 52 419 12286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008312233
X-RAY DIFFRACTIONf_angle_d0.990816778
X-RAY DIFFRACTIONf_chiral_restr0.05321846
X-RAY DIFFRACTIONf_plane_restr0.00781994
X-RAY DIFFRACTIONf_dihedral_angle_d18.91581984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.590.29981150.242308X-RAY DIFFRACTION86.35
2.59-2.640.28741320.21422514X-RAY DIFFRACTION93.83
2.64-2.690.2971470.20962573X-RAY DIFFRACTION97.18
2.69-2.750.29791540.21242602X-RAY DIFFRACTION97.94
2.75-2.810.3061320.21162639X-RAY DIFFRACTION98.96
2.81-2.870.27011250.21882695X-RAY DIFFRACTION99.09
2.87-2.940.32051430.21762610X-RAY DIFFRACTION99.35
2.94-3.020.26091430.21832704X-RAY DIFFRACTION99.34
3.02-3.110.26391370.222641X-RAY DIFFRACTION99.25
3.11-3.210.29421440.20812679X-RAY DIFFRACTION99.65
3.21-3.330.28811370.19972678X-RAY DIFFRACTION99.79
3.33-3.460.28321270.19672693X-RAY DIFFRACTION99.75
3.46-3.620.24471210.1852724X-RAY DIFFRACTION99.89
3.62-3.810.22721490.16942692X-RAY DIFFRACTION99.96
3.81-4.050.20381450.15882709X-RAY DIFFRACTION99.72
4.05-4.360.18391460.14722701X-RAY DIFFRACTION99.82
4.36-4.80.18411270.14472738X-RAY DIFFRACTION99.79
4.8-5.490.18051660.15572723X-RAY DIFFRACTION99.79
5.49-6.920.25381380.1852769X-RAY DIFFRACTION99.79
6.92-49.170.18381380.15172847X-RAY DIFFRACTION97.68
Refinement TLS params.Method: refined / Origin x: 9.85819719049 Å / Origin y: 69.3043024957 Å / Origin z: 90.020295974 Å
111213212223313233
T0.189080319426 Å2-0.0276074191852 Å2-0.0143886967063 Å2-0.195942062481 Å2-0.00168102216823 Å2--0.249293598244 Å2
L0.320288680617 °2-0.203056544842 °20.0108073740669 °2-0.654446865931 °2-0.288321019383 °2--0.941858894211 °2
S0.0195022280292 Å °-0.0231716713529 Å °0.00897028120435 Å °0.018618342732 Å °0.080764075269 Å °0.188775421311 Å °0.0212828647109 Å °-0.078594900022 Å °-0.0673315787679 Å °
Refinement TLS groupSelection details: all

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