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- PDB-8s9o: DNA cytosine-N4 methyltransferase (residues 61-324) from the Bdel... -

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Basic information

Entry
Database: PDB / ID: 8s9o
TitleDNA cytosine-N4 methyltransferase (residues 61-324) from the Bdelloid rotifer Adineta vaga - P1 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: 1.94 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
B: DNA cytosine-N4 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,33816
Polymers63,8302
Non-polymers1,50814
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint24 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.646, 53.301, 54.376
Angle α, β, γ (deg.)97.040, 104.340, 98.200
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein DNA cytosine-N4 methyltransferase


Mass: 31915.170 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium thiocyanate, 20 % 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: 1.94→51.96 Å / Num. obs: 38198 / % possible obs: 97.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.113 / Net I/σ(I): 3.6
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1866 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→26.02 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.9672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 1917 5.05 %
Rwork0.2058 36027 -
obs0.208 37944 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.48 Å2
Refinement stepCycle: LAST / Resolution: 1.94→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 102 177 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283782
X-RAY DIFFRACTIONf_angle_d0.58755131
X-RAY DIFFRACTIONf_chiral_restr0.0421566
X-RAY DIFFRACTIONf_plane_restr0.0041674
X-RAY DIFFRACTIONf_dihedral_angle_d12.07451387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.41331310.38172430X-RAY DIFFRACTION90.24
1.98-2.040.41461220.36732526X-RAY DIFFRACTION95.08
2.04-2.10.38141320.32782548X-RAY DIFFRACTION95.89
2.1-2.160.30621370.29912599X-RAY DIFFRACTION96.3
2.16-2.240.31271330.27772580X-RAY DIFFRACTION97.21
2.24-2.330.27041340.2452583X-RAY DIFFRACTION97.17
2.33-2.440.31371380.23122581X-RAY DIFFRACTION97.25
2.44-2.570.26721400.22242588X-RAY DIFFRACTION97.36
2.57-2.730.26041370.21482611X-RAY DIFFRACTION97.65
2.73-2.940.27421360.2082611X-RAY DIFFRACTION97.62
2.94-3.230.25551400.19282600X-RAY DIFFRACTION97.72
3.23-3.70.18871500.18182572X-RAY DIFFRACTION97.21
3.7-4.660.20991490.15032581X-RAY DIFFRACTION97.01
4.66-26.020.20651380.16992617X-RAY DIFFRACTION97.87
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)
13.22754380516-0.4648259119730.05191421838074.924192902070.07189898976124.3160883467-0.02273478868130.5695734012240.124858889702-0.4708582440610.0979745419889-0.277930630102-0.2823904897610.486726400654-0.07486157141990.282781102284-0.03493911023690.01201281692460.3141873642-0.03222564187570.21973986990514.4105019726-2.72987600203-2.30956068105
23.574705665290.1653333968521.192962612870.6828778606340.5884202100122.79884072626-0.01461506841190.148402620329-0.250928788343-0.0631324238130.116980086249-0.144367150040.08175774180210.176477963599-0.09404190455050.200260903271-0.03149456014070.003902166069890.257561689321-0.09197944713140.28131800919618.2332474992-10.08680152919.94381235118
30.692013151977-1.25624636802-0.5742514110752.46032306032.119655337796.969674091440.0224349812044-0.3530457926181.022793605770.1766673200170.177369903821-0.879691371003-1.20023187210.768626119314-0.1973044981490.542183471039-0.124733565756-0.03762840780150.480060871422-0.1956858668020.69997596255247.941930114220.993908467227.4824835342
44.24253381538-0.01808671651191.734661914335.89862474854-3.760254228177.19176417387-0.2889155663610.188511624065-0.2129742395580.04378047070620.05327799319861.61887163848-1.06844320453-1.181826785480.2374289787150.5181708998050.104423191745-0.1204453247660.499144171782-0.2767604281270.62042601996932.353439752115.740116196125.6193365836
55.33385891002-0.0461996841978-2.137286810076.65644578731-0.9507120325996.18591571834-0.1863447986180.2775373737880.822307414432-0.31367991090.2436606741830.754073387468-1.08631471895-0.695408700374-0.05151222683160.4376796632330.0545771330656-0.1455601541540.346388489756-0.04128559802550.39663487283337.360483305515.648094154118.5895448004
62.580788678441.100439921910.4152797324442.140185295560.8688420551171.112600168440.00846943602901-0.3652644376140.2604899235620.0683638550545-0.07727847169920.13212309218-0.0838721076919-0.1378757125580.05924636568670.2022284151870.0214899355347-0.04058262535440.380798252684-0.1217239035980.32101061078137.85462436355.1096605129328.4056717819
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 67 through 175 )AB67 - 1752 - 82
22chain 'A' and (resid 176 through 324 )AB176 - 32483 - 231
33chain 'B' and (resid 73 through 102 )BK73 - 1022 - 31
44chain 'B' and (resid 103 through 135 )BK103 - 13532 - 43
55chain 'B' and (resid 136 through 175 )BK136 - 17544 - 74
66chain 'B' and (resid 176 through 325 )BK176 - 32575 - 224

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