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- PDB-1aqi: STRUCTURE OF ADENINE-N6-DNA-METHYLTRANSFERASE TAQI -

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Basic information

Entry
Database: PDB / ID: 1aqi
TitleSTRUCTURE OF ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
ComponentsADENINE-N6-DNA-METHYLTRANSFERASE TAQI
KeywordsMETHYLTRANSFERASE / TRANSFERASE / RESTRICTION SYSTEM
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / Type II restriction enzyme and methyltransferase RM.Eco57I-like / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Eco57I restriction-modification methylase / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site ...Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / Type II restriction enzyme and methyltransferase RM.Eco57I-like / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Eco57I restriction-modification methylase / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Type II methyltransferase M.TaqI
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsSchluckebier, G. / Saenger, W.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI.
Authors: Schluckebier, G. / Kozak, M. / Bleimling, N. / Weinhold, E. / Saenger, W.
#1: Journal: Gene / Year: 1995
Title: A Model for DNA Binding and Enzyme Action Derived from Crystallographic Studies of the TaqI N6-Adenine-Methyltransferase
Authors: Schluckebier, G. / Labahn, J. / Granzin, J. / Schildkraut, I. / Saenger, W.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Universal Catalytic Domain Structure of Adomet-Dependent Methyltransferases
Authors: Schluckebier, G. / O'Gara, M. / Saenger, W. / Cheng, X.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-Dimensional Structure of the Adenine-Specific DNA Methyltransferase M.Taq I in Complex with the Cofactor S-Adenosylmethionine
Authors: Labahn, J. / Granzin, J. / Schluckebier, G. / Robinson, D.P. / Jack, W.E. / Schildkraut, I. / Saenger, W.
History
DepositionJul 25, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _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
A: ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
B: ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6314
Polymers95,8622
Non-polymers7692
Water1,22568
1
A: ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3162
Polymers47,9311
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENINE-N6-DNA-METHYLTRANSFERASE TAQI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3162
Polymers47,9311
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.080, 144.060, 53.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99993, 0.0114, 0.00167), (-0.0114, -0.99993, 0.00339), (0.00171, 0.00337, 0.99999)
Vector: 41.18, 78.28, 26.56)

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Components

#1: Protein ADENINE-N6-DNA-METHYLTRANSFERASE TAQI


Mass: 47931.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: PPR594 / Production host: Escherichia coli (E. coli) / Strain (production host): ER1821
References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.00065 mMM.TaqI1drop
21 mMSinefungin1dropcan be replaced by AdoHcy
30.1 mMduplex oligonucleotides1drop
4200 mM1dropNaCl
520 mMTris-HCl1drop
62-6 %PEG60001reservoir
7100 mM1reservoirNaCl
820 mMTris-HCl1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. obs: 30844 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Num. measured all: 110392

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→10 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.281 -10 %RANDOM
Rwork0.219 ---
obs0.219 30330 96 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 52 68 6322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.57
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_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23

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