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- PDB-8s9m: DNA cytosine-N4 methyltransferase (residues 79-324) from the Bdel... -

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Basic information

Entry
Database: PDB / ID: 8s9m
TitleDNA cytosine-N4 methyltransferase (residues 79-324) from the Bdelloid rotifer Adineta vaga
ComponentsDNA cytosine-N4 methyltransferase
KeywordsTRANSFERASE/INHIBITOR / DNA Cytosine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / TRANSFERASE-INHIBITOR complex
Function / homologySINEFUNGIN
Function and homology information
Biological speciesAdineta vaga (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsZhou, J. / Horton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga.
Authors: Zhou, J. / Horton, J.R. / Kaur, G. / Chen, Q. / Li, X. / Mendoza, F. / Wu, T. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionMar 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA cytosine-N4 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,74811
Polymers29,8081
Non-polymers94010
Water3,027168
1
A: DNA cytosine-N4 methyltransferase
hetero molecules

A: DNA cytosine-N4 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,49622
Polymers59,6162
Non-polymers1,88020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)57.581, 69.096, 124.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-624-

HOH

31A-632-

HOH

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Components

#1: Protein DNA cytosine-N4 methyltransferase


Mass: 29807.803 Da / Num. of mol.: 1 / Fragment: Methyltransferase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adineta vaga (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium citrate tribasic monohydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→41.68 Å / Num. obs: 40906 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 11.81 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.084 / Net I/σ(I): 9.9
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4026 / CC1/2: 0.34 / Rpim(I) all: 0.78 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→41.68 Å / SU ML: 0.1324 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 2000 4.9 %
Rwork0.1599 38847 -
obs0.1617 40847 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.48 Å2
Refinement stepCycle: LAST / Resolution: 1.49→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 63 168 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482140
X-RAY DIFFRACTIONf_angle_d0.78322903
X-RAY DIFFRACTIONf_chiral_restr0.0772307
X-RAY DIFFRACTIONf_plane_restr0.0068383
X-RAY DIFFRACTIONf_dihedral_angle_d11.5272821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.26351380.22082687X-RAY DIFFRACTION98.12
1.53-1.570.23461420.1892750X-RAY DIFFRACTION99.83
1.57-1.610.19741410.1712755X-RAY DIFFRACTION99.97
1.61-1.670.20721430.15952752X-RAY DIFFRACTION99.9
1.67-1.730.19651410.15762759X-RAY DIFFRACTION99.79
1.73-1.80.17891420.14672740X-RAY DIFFRACTION99.97
1.8-1.880.17851420.14152747X-RAY DIFFRACTION99.97
1.88-1.980.14851420.13722770X-RAY DIFFRACTION99.9
1.98-2.10.20451410.14562760X-RAY DIFFRACTION99.93
2.1-2.260.17921440.14422787X-RAY DIFFRACTION100
2.26-2.490.19461440.15182794X-RAY DIFFRACTION100
2.49-2.850.18981430.1662788X-RAY DIFFRACTION99.9
2.85-3.590.2091460.16862823X-RAY DIFFRACTION99.87
3.59-41.680.20791510.16672935X-RAY DIFFRACTION99.74

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