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- PDB-1dct: DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1dct
TitleDNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA
Components
  • DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3')
  • PROTEIN (MODIFICATION METHYLASE HAEIII)
KeywordsTRANSFERASE/DNA / ENZYME / CYTOSINE METHYLASE / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / negative regulation of gene expression via chromosomal CpG island methylation / methylation / DNA binding / ATP 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
DNA / DNA (> 10) / Type II methyltransferase M.HaeIII
Similarity search - Component
Biological speciesHaemophilus influenzae biotype aegyptius (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsReinisch, K.M. / Chen, L. / Verdine, G.L. / Lipscomb, W.N.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
Authors: Reinisch, K.M. / Chen, L. / Verdine, G.L. / Lipscomb, W.N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Prelimanary Crystallographic Analysis of a DNA (Cytosine-5) -Methyltransferase from Haemophilus Aegyptius Bound Covalently to DNA
Authors: Reinisch, K.M. / Chen, L. / Verdine, G.L. / Lipscomb, W.N.
History
DepositionMay 17, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
F: DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3')
M: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3')
G: DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3')
N: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3')
A: PROTEIN (MODIFICATION METHYLASE HAEIII)
B: PROTEIN (MODIFICATION METHYLASE HAEIII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4948
Polymers96,4146
Non-polymers802
Water00
1
F: DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3')
M: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3')
A: PROTEIN (MODIFICATION METHYLASE HAEIII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2474
Polymers48,2073
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3')
N: DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3')
B: PROTEIN (MODIFICATION METHYLASE HAEIII)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2474
Polymers48,2073
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.570, 108.040, 155.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsTHIS FILE CONTAINS 2 PROTEIN-DNA COMPLEXES IN THE ASYMMETRIC UNIT. PROTEIN MONOMER A IS COVALENTLY BOUND TO A DNA DUPLEX CONSISTING OF CHAINS F AND M, AND PROTEIN MONOMER B IS COVALENTLY LINKED TO A DUPLEX CONSISTING OF CHAINS G AND N. THERE ARE TWO SPECIAL NUCLEOTIDE BASES INCORPORATED INTO EACH DNA DUPLEX - ONE IRREGULAR BASE IN EACH CHAIN. ONE OF THESE BASES IS A CYTOSINE METHYLATED AT THE 5-POSITION, AND THE OTHER (DESCRIBED IN MORE DETAIL BELOW) IS USED TO COVALENTLY LINK THE DNA TO THE PROTEIN. THE DNA AT THE RECOGNITION SITE IS VERY DISTORTED: THERE IS AN EXTRAHELICAL CYTOSINE (THE MODIFIED ONE COVALENTLY LINKED TO THE PROTEIN VIA CYS 71: +C F 10 AND +C G 10) AND BASE PAIRING IN THE DNA RECOGNITION SEQUENCE IS REORGANIZED. THERE ARE ALSO TWO CA+2 IONS IN THE ASYMMETRIC UNIT.

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3')


Mass: 5559.653 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3')


Mass: 5553.590 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein PROTEIN (MODIFICATION METHYLASE HAEIII) / E.C.2.1.1.73 / CYTOSINE-SPECIFIC METHYLTRANSFERASE / HAEIII / M.HAEIII


Mass: 37093.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Haemophilus influenzae biotype aegyptius (bacteria)
Species: Haemophilus influenzae / Strain: biotype aegyptius / References: UniProt: P20589, EC: 2.1.1.73
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 350011
3GLYCEROL11
4CACL211
5MES11
6DTT11
7WATER12
8PEG 350012
9GLYCEROL12
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1reservoirpH6.5
2120 mM1reservoirCaCl2
39-13 %PEG35001reservoir
413 %glycerol1reservoir
51 mMdithiothreitol1reservoir
61
71
81
91

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. all: 129524 / Num. obs: 26866 / % possible obs: 95 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 95 % / Observed criterion σ(I): 1 / Num. measured all: 129524

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Processing

Software
NameClassification
R-AXISdata collection
X-PLORrefinement
R-AXISdata reduction
RefinementResolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection
Rfree0.326 -
Rwork0.226 -
obs0.226 22801
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 1408 8 0 6914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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