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

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Basic information

Entry
Database: PDB / ID: 8cxu
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 2
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
: / N-[(4-aminophenyl)methyl]adenosine / 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: 2.28 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

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)
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)234,22527
Polymers232,3379
Non-polymers1,88718
Water10,629590
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)78,0218
Polymers77,4463
Non-polymers5755
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-22 kcal/mol
Surface area26820 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)78,30813
Polymers77,4463
Non-polymers86210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-20 kcal/mol
Surface area26840 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)77,8966
Polymers77,4463
Non-polymers4513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-30 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.446, 161.237, 229.523
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 / 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 / DNA


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


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, 608 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-T96 / N-[(4-aminophenyl)methyl]adenosine


Mass: 372.379 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H20N6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 3.24 Å3/Da / Density % sol: 62.08 %
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: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→44.86 Å / Num. obs: 129038 / % possible obs: 93.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 38.36 Å2 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.072 / Net I/σ(I): 10
Reflection shellResolution: 2.28→2.37 Å / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 10190 / CC1/2: 0.41 / CC star: 0.762 / Rpim(I) all: 0.733 / % possible all: 74.8

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Processing

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

7lnj


Resolution: 2.28→44.86 Å / SU ML: 0.3167 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 1998 1.55 %
Rwork0.1874 126739 -
obs0.1879 128737 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.16 Å2
Refinement stepCycle: LAST / Resolution: 2.28→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13399 1704 120 590 15813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002615706
X-RAY DIFFRACTIONf_angle_d0.532121515
X-RAY DIFFRACTIONf_chiral_restr0.04182357
X-RAY DIFFRACTIONf_plane_restr0.00332458
X-RAY DIFFRACTIONf_dihedral_angle_d16.58246006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.41641000.40316337X-RAY DIFFRACTION65.63
2.34-2.40.38711230.32167830X-RAY DIFFRACTION81.15
2.4-2.470.341340.28788492X-RAY DIFFRACTION88.17
2.47-2.550.28421410.2838896X-RAY DIFFRACTION92.05
2.55-2.640.28021420.26789012X-RAY DIFFRACTION93.27
2.64-2.750.28831380.23538796X-RAY DIFFRACTION91.37
2.75-2.870.26631470.22679252X-RAY DIFFRACTION95.27
2.87-3.020.26661490.2189502X-RAY DIFFRACTION97.85
3.02-3.210.25051520.21729586X-RAY DIFFRACTION98.89
3.21-3.460.23321520.17879665X-RAY DIFFRACTION99.48
3.46-3.810.2021530.16179750X-RAY DIFFRACTION99.6
3.81-4.360.17561520.1399594X-RAY DIFFRACTION97.76
4.36-5.490.16311560.13169913X-RAY DIFFRACTION100
5.49-44.860.15931590.154610114X-RAY DIFFRACTION98.82
Refinement TLS params.Method: refined / Origin x: -0.733466371478 Å / Origin y: 4.12094265208 Å / Origin z: -19.9618371531 Å
111213212223313233
T0.158794218987 Å20.0180855132564 Å20.0103316054037 Å2-0.166524941867 Å20.0139665254804 Å2--0.172386334827 Å2
L0.0159052180092 °20.0182943832468 °2-0.0538895186129 °2-0.117109661549 °2-0.0924932636238 °2--0.116906019072 °2
S0.0268855319712 Å °-0.0210140069205 Å °0.0365869501176 Å °0.00993844950037 Å °-0.0369860236354 Å °-0.0115014365118 Å °-0.0602106471108 Å °-0.0228472602045 Å °-0.00312192268693 Å °
Refinement TLS groupSelection details: all

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