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- PDB-8yf3: DNA cytosine C5-carboxymethyltransferase in complex with Cx-SAM -

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Basic information

Entry
Database: PDB / ID: 8yf3
TitleDNA cytosine C5-carboxymethyltransferase in complex with Cx-SAM
ComponentsCytosine-specific methyltransferase
KeywordsTRANSFERASE / DNA cytosine-5-carboxymethyltransferase / Carboxy-SAM
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / methylation / symbiont-mediated suppression of host innate immune response
Similarity search - Function
: / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-GEK / Cytosine-specific methyltransferase
Similarity search - Component
Biological speciesSynechococcus phage S-B43 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, Q. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: DNA cytosine-5-carboxymethyltransferase in complex with Cx-SAM
Authors: Yang, Q. / Zhang, Y.
History
DepositionFeb 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosine-specific methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4042
Polymers40,9621
Non-polymers4421
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.261, 42.131, 98.003
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytosine-specific methyltransferase


Mass: 40961.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus phage S-B43 (virus) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A514ABG7, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-GEK / (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate / CARBOXY-S-ADENOSYLMETHIONINE


Mass: 442.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N6O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BICINE, 20% (w/v) PEG 6000, 1 mM S-adenosyl-S-carboxymethyl-L-homocysteine (Cx-SAM)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→48.73 Å / Num. obs: 25592 / % possible obs: 97.3 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.106 / Rrim(I) all: 0.265 / Χ2: 0.92 / Net I/σ(I): 5.3 / Num. measured all: 159146
Reflection shellResolution: 1.9→2 Å / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 2.275 / Num. measured all: 19275 / Num. unique obs: 3811 / CC1/2: 0.425 / Rpim(I) all: 1.136 / Rrim(I) all: 2.554 / Χ2: 0.91 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.73 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 32.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1273 5 %
Rwork0.2151 --
obs0.2176 25474 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 30 165 2778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072663
X-RAY DIFFRACTIONf_angle_d0.8363600
X-RAY DIFFRACTIONf_dihedral_angle_d15.5361011
X-RAY DIFFRACTIONf_chiral_restr0.051412
X-RAY DIFFRACTIONf_plane_restr0.007455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.4461490.38082667X-RAY DIFFRACTION98
1.97-2.060.39211420.31392725X-RAY DIFFRACTION99
2.06-2.170.30011410.27812772X-RAY DIFFRACTION100
2.17-2.310.33961360.25512578X-RAY DIFFRACTION94
2.31-2.480.27471490.22422761X-RAY DIFFRACTION100
2.48-2.730.27041470.21972757X-RAY DIFFRACTION100
2.73-3.130.27521430.20082785X-RAY DIFFRACTION100
3.13-3.940.22291350.18422269X-RAY DIFFRACTION82
3.94-48.730.18621310.16292887X-RAY DIFFRACTION100

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