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

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Basic information

Entry
Database: PDB / ID: 7rfn
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor SGC8158
Components
  • DNA Strand 1DNA
  • DNA Strand 2DNA
  • Site-specific DNA-methyltransferase (adenine-specific)DNA methyltransferase
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


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA binding
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / 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-MJ7 / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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)234,89729
Polymers232,3379
Non-polymers2,56020
Water7,566420
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)78,2038
Polymers77,4463
Non-polymers7575
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-23 kcal/mol
Surface area26810 Å2
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)78,42912
Polymers77,4463
Non-polymers9839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-22 kcal/mol
Surface area27070 Å2
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)78,2659
Polymers77,4463
Non-polymers8196
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-19 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.831, 161.354, 229.908
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) / DNA 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 / DNA


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


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, 440 molecules

#4: Chemical ChemComp-MJ7 / 5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl)methyl]amino}butyl)-5'-thioadenosine


Mass: 555.091 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H31ClN6O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.27 Å3/Da / Density % sol: 62.34 %
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: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.03 Å / Num. obs: 105380 / % possible obs: 99.3 % / Redundancy: 12.6 % / Biso Wilson estimate: 51.44 Å2 / Rmerge(I) obs: 0.301 / Rpim(I) all: 0.084 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.92 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 10298 / CC1/2: 0.397 / Rpim(I) all: 0.709 / % possible all: 98.2

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Processing

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

7lt5


Resolution: 2.5→47.03 Å / SU ML: 0.3503 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 1999 1.9 %
Rwork0.195 103168 -
obs0.1957 105167 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13306 1704 161 420 15591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002215653
X-RAY DIFFRACTIONf_angle_d0.476721457
X-RAY DIFFRACTIONf_chiral_restr0.042352
X-RAY DIFFRACTIONf_plane_restr0.00282392
X-RAY DIFFRACTIONf_dihedral_angle_d16.20715879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.40381320.35866803X-RAY DIFFRACTION91.95
2.56-2.630.38081400.3127292X-RAY DIFFRACTION99.35
2.63-2.70.30681420.28747315X-RAY DIFFRACTION99.11
2.7-2.790.31261400.28427186X-RAY DIFFRACTION97.63
2.79-2.890.31961430.27577374X-RAY DIFFRACTION99.88
2.89-3.010.31381430.25067414X-RAY DIFFRACTION99.84
3.01-3.140.28941450.22787419X-RAY DIFFRACTION99.97
3.14-3.310.24171420.21487385X-RAY DIFFRACTION99.92
3.31-3.520.22941440.19557434X-RAY DIFFRACTION99.87
3.52-3.790.22011440.17497429X-RAY DIFFRACTION99.74
3.79-4.170.17371420.15787308X-RAY DIFFRACTION97.51
4.17-4.770.21681450.14467509X-RAY DIFFRACTION99.79
4.77-6.010.15061480.16417580X-RAY DIFFRACTION99.91
6.01-47.030.21251490.17387720X-RAY DIFFRACTION98.08

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