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- PDB-8cxt: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 8cxt
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor N6-benzyladenosine (Compound 1)
Components
  • DNA Strand 1
  • DNA Strand 2
  • Site-specific DNA-methyltransferase (adenine-specific)
KeywordsDNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / 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
: / N-benzyladenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile 630 (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.61 Å
AuthorsHorton, J.R. / Zhou, J. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / ...Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / Mai, A. / Rotili, D. / Cheng, X.
History
DepositionMay 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 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

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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-methyltransferase (adenine-specific)
D: DNA Strand 1
E: DNA Strand 2
F: DNA Strand 1
G: DNA Strand 2
H: DNA Strand 1
I: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,74520
Polymers232,3379
Non-polymers1,40811
Water2,288127
1
A: Site-specific DNA-methyltransferase (adenine-specific)
D: DNA Strand 1
E: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8816
Polymers77,4463
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA Strand 1
G: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9838
Polymers77,4463
Non-polymers5375
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA Strand 1
I: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8816
Polymers77,4463
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.213, 161.667, 230.797
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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Protein , 1 types, 3 molecules ABC

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


Mass: 68887.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 630 (bacteria)
Strain: 630 / Gene: CD630_27580 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q183J3, site-specific DNA-methyltransferase (adenine-specific)

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DNA chain , 2 types, 6 molecules DFHEGI

#2: DNA chain DNA Strand 1


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA Strand 2


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)

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Non-polymers , 4 types, 138 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-Q8C / N-benzyladenosine


Mass: 357.364 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H19N5O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 21~24% (w/v) polyethylene glycol 3350, 0.1 M Tris-HCl pH 7.0~7.5, 0.28 M potassium citrate
PH range: 7.0-7.5

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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: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→44.23 Å / Num. obs: 91039 / % possible obs: 100 % / Redundancy: 23.8 % / Biso Wilson estimate: 63.41 Å2 / Rmerge(I) obs: 0.337 / Rpim(I) all: 0.063 / Net I/σ(I): 11.3
Reflection shellResolution: 2.61→2.74 Å / Rmerge(I) obs: 2.124 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8954 / CC1/2: 0.468 / CC star: 0.799 / Rpim(I) all: 0.678 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNJ

7lnj


Resolution: 2.61→44.23 Å / SU ML: 0.3975 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 2000 2.2 %
Rwork0.1894 88810 -
obs0.1901 90810 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.75 Å2
Refinement stepCycle: LAST / Resolution: 2.61→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13233 1686 89 127 15135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002615491
X-RAY DIFFRACTIONf_angle_d0.558821255
X-RAY DIFFRACTIONf_chiral_restr0.04312345
X-RAY DIFFRACTIONf_plane_restr0.00352433
X-RAY DIFFRACTIONf_dihedral_angle_d17.0465877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.680.3677770.32533450X-RAY DIFFRACTION53.31
2.68-2.750.3771470.30776501X-RAY DIFFRACTION99.8
2.75-2.830.35221460.28726465X-RAY DIFFRACTION99.86
2.83-2.920.30451450.28146478X-RAY DIFFRACTION99.82
2.92-3.030.34431470.28176504X-RAY DIFFRACTION99.98
3.03-3.150.26751460.24976487X-RAY DIFFRACTION99.97
3.15-3.290.31721470.23336533X-RAY DIFFRACTION99.99
3.29-3.470.24921470.20666515X-RAY DIFFRACTION99.97
3.47-3.680.23941470.18886529X-RAY DIFFRACTION99.99
3.68-3.970.24931470.17696561X-RAY DIFFRACTION99.97
3.97-4.370.17431490.15016581X-RAY DIFFRACTION99.96
4.37-50.17751480.13876596X-RAY DIFFRACTION100
5-6.290.16751510.16526699X-RAY DIFFRACTION100
6.29-44.230.18261560.17126911X-RAY DIFFRACTION99.89

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