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- PDB-2zcj: Ternary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyl... -

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Basic information

Entry
Database: PDB / ID: 2zcj
TitleTernary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy
Components
  • DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')
  • DNA (5'-D(*DTP*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')
  • Modification methylase HhaI
KeywordsTRANSFERASE/DNA / Alpha and beta / 3-layer Sandwich / Methyltransferase / Restriction system / S-adenosyl-L-methionine / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Type II methyltransferase M.HhaI
Similarity search - Component
Biological speciesHaemophilus parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / simulation annealing / Resolution: 2.75 Å
AuthorsShieh, F.K. / Reich, N.O.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI
Authors: Shieh, F.K. / Reich, N.O.
History
DepositionNov 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')
D: DNA (5'-D(*DTP*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')
A: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0554
Polymers44,6703
Non-polymers3841
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.470, 98.470, 321.615
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: DNA chain DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Construction
#2: DNA chain DNA (5'-D(*DTP*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3')


Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Construction
#3: Protein Modification methylase HhaI / Cytosine-specific methyltransferase HhaI / M.HhaI


Mass: 37041.223 Da / Num. of mol.: 1 / Mutation: E119Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria)
Gene: hhaIM / Plasmid: pHSHW-5 / Production host: Escherichia coli (E. coli)
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Sodium Citrate, 1.6-2.1 Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2ammonium sulfate11
3H2O11
4sodium citrate12
5ammonium sulfate12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 18897 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.106 / Rsym value: 0.071
Reflection shellResolution: 2.6→2.75 Å / Rmerge(I) obs: 0.365 / Num. unique all: 2691 / Rsym value: 0.509

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: simulation annealing / Resolution: 2.75→8.64 Å / σ(F): 2 / σ(I): 2 /
RfactorNum. reflection
Rfree0.266 -
Rwork0.218 -
obs-16061
Refinement stepCycle: LAST / Resolution: 2.75→8.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 506 26 72 3210
LS refinement shellResolution: 2.75→2.78 Å /
RfactorNum. reflection
Rfree0.34 -
Rwork0.293 -
obs-53

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