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- PDB-8s9n: DNA cytosine-N4 methyltransferase (residues 61-324) from the Bdel... -

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Basic information

Entry
Database: PDB / ID: 8s9n
TitleDNA cytosine-N4 methyltransferase (residues 61-324) from the Bdelloid rotifer Adineta vaga - C2 crystal form
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: 1.89 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

Downloads & links

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Assembly

Deposited unit
A: DNA cytosine-N4 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5456
Polymers31,9151
Non-polymers6305
Water1,18966
1
A: DNA cytosine-N4 methyltransferase
hetero molecules

A: DNA cytosine-N4 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,09012
Polymers63,8302
Non-polymers1,25910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4350 Å2
ΔGint6 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.426, 82.285, 49.773
Angle α, β, γ (deg.)90.000, 106.570, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-555-

HOH

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Components

#1: Protein DNA cytosine-N4 methyltransferase


Mass: 31915.170 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.89→52.63 Å / Num. obs: 21990 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 40.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.05 / Net I/σ(I): 6.8
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1082 / CC1/2: 0.435 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→34.23 Å / SU ML: 0.2639 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.4711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 1094 5.05 %
Rwork0.2008 20559 -
obs0.2022 21653 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.3 Å2
Refinement stepCycle: LAST / Resolution: 1.89→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 43 66 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371872
X-RAY DIFFRACTIONf_angle_d0.65492542
X-RAY DIFFRACTIONf_chiral_restr0.0456278
X-RAY DIFFRACTIONf_plane_restr0.0058335
X-RAY DIFFRACTIONf_dihedral_angle_d11.85682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.980.38631420.40682296X-RAY DIFFRACTION89.37
1.98-2.080.40111320.35382592X-RAY DIFFRACTION98.41
2.08-2.210.35051340.30612583X-RAY DIFFRACTION99.38
2.21-2.380.26841540.24622580X-RAY DIFFRACTION99.27
2.38-2.620.2421460.21892587X-RAY DIFFRACTION99.93
2.62-30.21661320.20252622X-RAY DIFFRACTION99.78
3-3.780.22851380.18752603X-RAY DIFFRACTION99.82
3.78-34.230.18291160.16362696X-RAY DIFFRACTION99.75
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)
13.838977561911.35652894213-0.6125103902965.578671448650.2483232724033.715715547570.292866670623-0.439887061525-0.6651781095830.560367546907-0.506357579431-0.2260527900980.8538047393690.8589940205570.2218881719530.6045789776840.113183552947-0.06489017430270.7809889945720.04211981565710.50446902391217.3637973809-0.26075189716828.6223703636
26.774152976690.430652454343-3.563116173913.59376285065-2.02523949966.13753814183-0.05271212822950.204920576673-1.01366123568-0.402234712654-0.0531950473462-0.2766470230451.230100187780.447380666610.07814443671340.5364168503370.124178324058-0.1395956733680.538927639203-0.05298046468370.52792930352712.1798729946-0.44913109532617.0962269459
33.43281320303-1.036450511551.866925599166.62949068921-2.462543749234.655184773260.4494563496230.321186680568-0.912891150944-0.845840476191-0.223429920907-0.4283160147051.19220969390.289550202653-0.198398132030.5840000333580.0647502850546-0.066710904460.436606367687-0.05118215573890.5717880537495.44566613971.0018467034210.698435941
42.19427338926-0.370791974194-1.113164375470.395827241614-0.849861538018.695218801830.1138368281210.0359431752806-0.119818891634-0.07206407967690.146222090944-0.04985830021940.1394141062830.184081670059-0.2678771625250.291712951602-0.01710690072350.0004399364800430.295843944253-0.02687529352690.3807704835251.9514721863313.21179707367.16654149092
59.81761491143-4.145570102451.902321805982.0647618453-6.061888351348.772336700930.6917803906660.5443080042721.218532862850.00964400058822-1.12154584157-1.87763076158-0.3090816783683.215586533590.5047963142410.64961985512-0.1032843291630.08002885416961.53519959353-0.05722687131810.76580964506917.2639791617.84538311778.1217657432
65.02705696881-0.07430377420160.3350934064233.14434518844-1.827851933566.366989651780.200226754863-0.4881594659890.07293439634230.0954101630571-0.0934074210209-0.277060816243-0.1582636790650.91752362043-0.1083820500460.308348737793-0.03579839055920.001269404909550.419351853059-0.04667735629020.30963453946511.430321988812.656616494320.9703643109
79.41863637449-6.030020949154.408917591296.44727123784-3.403402633685.83426263097-0.2103708034770.2156769651160.7675480845240.111203448777-0.0645827765306-0.924834245103-0.6495147354831.610818570950.4041318661120.466942325814-0.1336031697960.0133240731570.8552120668620.05060001232790.53120270439620.697958158818.206494686519.8430192617
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: B

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 68 through 88 )68 - 882 - 22
22chain 'A' and (resid 89 through 137 )89 - 13723 - 47
33chain 'A' and (resid 138 through 194 )138 - 19448 - 95
44chain 'A' and (resid 195 through 244 )195 - 24496 - 145
55chain 'A' and (resid 245 through 258 )245 - 258146 - 159
66chain 'A' and (resid 259 through 303 )259 - 303160 - 204
77chain 'A' and (resid 304 through 324 )304 - 324205 - 225

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