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- PDB-1q0t: Ternary Structure of T4DAM with AdoHcy and DNA -

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Basic information

Entry
Database: PDB / ID: 1q0t
TitleTernary Structure of T4DAM with AdoHcy and DNA
Components
  • 5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'
  • DNA adenine methylase
KeywordsTransferase/DNA / T4DAM / Methyltransferase / DNA / Transferase-DNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA replication / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / DNA binding
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA adenine methylase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsYang, Z. / Horton, J.R. / Zhou, L. / Zhang, X.J. / Dong, A. / Zhang, X. / Schlagman, S.L. / Kossykh, V. / Hattman, S. / Cheng, X.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of the bacteriophage T4 DNA adenine methyltransferase
Authors: Yang, Z. / Horton, J.R. / Zhou, L. / Zhang, X.J. / Dong, A. / Zhang, X. / Schlagman, S.L. / Kossykh, V. / Hattman, S. / Cheng, X.
History
DepositionJul 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 22, 2020Group: Derived calculations
Category: ndb_struct_na_base_pair / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _ndb_struct_na_base_pair.buckle
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'
D: 5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'
A: DNA adenine methylase
B: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2758
Polymers68,2524
Non-polymers1,0234
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.7, 109.7, 73.6
Angle α, β, γ (deg.)90.0, 104.2, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Palindromic 12 Base Pair DNA Duplex
#2: Protein DNA adenine methylase / 2.1.1.72 / Deoxyadenosyl-methyltransferase / M.EcoT4Dam


Mass: 30463.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: DAM / Plasmid: PJW2 / Production host: Escherichia coli (E. coli)
References: UniProt: P04392, site-specific DNA-methyltransferase (adenine-specific)
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2ammonium sulfate11
3H2O11
4PEG 800012
5ammonium sulfate12
6H2O12
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlprotein1drop
22.4 M1reservoir
3100 mMMES1reservoirpH6.0
41
51
61

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 11204 / Num. obs: 11038 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.9
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 8.6 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 43112
Reflection shell
*PLUS
Highest resolution: 3.1 Å / % possible obs: 97.3 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 554 5 %RANDOM
Rwork0.238 ---
obs-10955 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.321 Å20 Å2-7.275 Å2
2--4.023 Å20 Å2
3---11.298 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 486 54 0 4538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it4.8511.5
X-RAY DIFFRACTIONc_scbond_it7.1232
X-RAY DIFFRACTIONc_mcangle_it7.4442
X-RAY DIFFRACTIONc_scangle_it9.9362.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3sam.par
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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