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- PDB-7rfl: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

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Basic information

Entry
Database: PDB / ID: 7rfl
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor SGC0946
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 modification / methylation / nucleic acid 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
Chem-AW2 / : / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHorton, J.R. / Cheng, X. / Zhou, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Epigenetics / Year: 2022
Title: Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
Authors: Zhou, J. / Horton, J.R. / Yu, D. / Ren, R. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 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

Downloads & links

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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)
E: DNA Strand 2
D: DNA Strand 1
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)234,88525
Polymers232,3379
Non-polymers2,54816
Water7,909439
1
A: Site-specific DNA-methyltransferase (adenine-specific)
E: DNA Strand 2
D: DNA Strand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3299
Polymers77,4463
Non-polymers8836
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)78,39110
Polymers77,4463
Non-polymers9457
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)78,1666
Polymers77,4463
Non-polymers7203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.442, 161.741, 229.853
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 (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 EGIDFH

#2: DNA chain DNA Strand 2


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA Strand 1


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

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Non-polymers , 4 types, 455 molecules

#4: Chemical ChemComp-AW2 / 5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 618.566 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H40BrN7O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
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: 7-7.5

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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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→41.87 Å / Num. obs: 111448 / % possible obs: 91.6 % / Redundancy: 10.8 % / Biso Wilson estimate: 44.91 Å2 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 2.38→2.48 Å / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9690 / CC1/2: 0.258 / Rpim(I) all: 0.615 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LT5

7lt5


Resolution: 2.38→41.87 Å / SU ML: 0.2826 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 1998 1.8 %
Rwork0.2042 109265 -
obs0.2047 111263 91.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.33 Å2
Refinement stepCycle: LAST / Resolution: 2.38→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13392 1686 157 439 15674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002515724
X-RAY DIFFRACTIONf_angle_d0.544921562
X-RAY DIFFRACTIONf_chiral_restr0.04192377
X-RAY DIFFRACTIONf_plane_restr0.00312396
X-RAY DIFFRACTIONf_dihedral_angle_d16.36075886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.32831180.29716478X-RAY DIFFRACTION76.63
2.44-2.510.28211240.28136812X-RAY DIFFRACTION80.83
2.51-2.580.34771310.27397148X-RAY DIFFRACTION84.43
2.58-2.670.32031350.27197315X-RAY DIFFRACTION86.54
2.67-2.760.30491350.27137406X-RAY DIFFRACTION87.39
2.76-2.870.28531380.25767564X-RAY DIFFRACTION88.94
2.87-30.29041410.25517703X-RAY DIFFRACTION90.72
3-3.160.30771430.25647836X-RAY DIFFRACTION92.4
3.16-3.360.31061490.24728143X-RAY DIFFRACTION95.37
3.36-3.620.21061490.20058143X-RAY DIFFRACTION95.24
3.62-3.980.22221540.18788448X-RAY DIFFRACTION98.85
3.98-4.560.18061580.16058615X-RAY DIFFRACTION99.8
4.56-5.740.19891590.16348688X-RAY DIFFRACTION99.99
5.74-41.870.18661640.17188966X-RAY DIFFRACTION99.65

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