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- PDB-2z6a: S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Pre... -

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Basic information

Entry
Database: PDB / ID: 2z6a
TitleS-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation
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 / Protein-DNA complex / Methyltransferase / Restriction system / S-adenosyl-L-methionine / Transferase / 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 ...: / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Simulation annealing / Resolution: 2.88 Å
AuthorsShieh, F.K.
CitationJournal: Biochemistry / Year: 2007
Title: S-Adenosyl-l-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation
Authors: Youngblood, B. / Shieh, F.K. / Buller, F. / Bullock, T. / Reich, N.O.
History
DepositionJul 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / reflns_shell
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 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 1.4Nov 1, 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
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)45,0244
Polymers44,6393
Non-polymers3841
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.490, 98.490, 323.610
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 / Source: (synth.) synthetic construct (others)
#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 / Source: (synth.) synthetic construct (others)
#3: Protein Modification methylase HhaI / HHAI METHYLTRANSFERASE / Cytosine-specific methyltransferase HhaI / M.HhaI


Mass: 37010.145 Da / Num. of mol.: 1 / Mutation: C81A
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.: 55 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M Ammonium Sulfate, 50mM Sodium Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2Sodium Citrate11
3H2O11
4Ammonium Sulfate12
5Sodium Citrate12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2005 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.88→20 Å / Num. obs: 14120 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique all: 2034 / Rsym value: 0.354 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: Simulation annealing
Starting model: PDB Entry 2HR1

2hr1


Resolution: 2.88→8.85 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.28 441 -
Rwork0.22 --
all0.297 --
obs0.239 12688 99.9 %
Refinement stepCycle: LAST / Resolution: 2.88→8.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 506 26 55 3192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_bond_d0.0074
LS refinement shellResolution: 2.88→2.92 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.435 350 -
Rwork0.345 --
obs-441 99.9 %

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