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- PDB-1g38: ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1g38
TitleADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX
Components
  • 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
  • 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'
  • MODIFICATION METHYLASE TAQI
KeywordsTRANSFERASE/DNA / TRANSFERASE / DNA / METHYLTRANSFERASE / RESTRICTION SYSTEM / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / N-6 Adenine-specific DNA methylases signature. ...Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / 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
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE / DNA / Type II methyltransferase M.TaqI
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGoedecke, K. / Pignot, M. / Goody, R.S. / Scheidig, A.J. / Weinhold, E.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.
Authors: Goedecke, K. / Pignot, M. / Goody, R.S. / Scheidig, A.J. / Weinhold, E.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: DIFFERENTIAL BINDING OF S-ADENOSYLMETHIONINE, S-ADENOSYLHOMOCYSTEINE AND SINEFUNGIN TO THE ADENINE-SPECIFIC DNA METHYLTRANSFERASE M. TAQ I
Authors: Schluckebier, G. / Kozak, M. / Bleimling, N. / Weinhold, E. / Saenger, W.
History
DepositionOct 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 28, 2013Group: Atomic model
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
B: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'
C: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
E: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'
F: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
A: MODIFICATION METHYLASE TAQI
D: MODIFICATION METHYLASE TAQI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8188
Polymers102,1666
Non-polymers6532
Water8,935496
1
B: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'
C: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
A: MODIFICATION METHYLASE TAQI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4094
Polymers51,0833
Non-polymers3261
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'
F: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
D: MODIFICATION METHYLASE TAQI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4094
Polymers51,0833
Non-polymers3261
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.500, 68.650, 114.430
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3051.001 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'


Mass: 3052.046 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein MODIFICATION METHYLASE TAQI / 2.1.1.72 / ADENINE-N6-DNA-METHYLTRANSFERASE TAQI


Mass: 44979.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 21 - 413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: PA1-MTAQ-A49A / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific)
#4: Chemical ChemComp-NEA / 5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE


Mass: 326.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N6O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.6 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% Isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutionsName: isopropanol
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.075 mMM-Taql1drop
20.100 mMoligodeoxynucleotide1drop
32 mMAETA1drop
410 mMTris-HCl1drop
5300 mM1dropNaCl
650 mMsodium cacodylate1reservoir
7100 mM1reservoirKCl
825 mM1reservoirMgCl2
915 %(v/v)iso-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 1999 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 218047 / Num. obs: 54457 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 10.42
Reflection shellResolution: 2→2.13 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.6 / Num. unique all: 8013 / Rsym value: 0.195 / % possible all: 67.1
Reflection
*PLUS
Num. measured all: 218047

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNSrefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ADM

2adm


Resolution: 2→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: isotropic / Cross valid method: CNS throughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5538 10.2 %RANDOM
Rwork0.196 ---
all0.208 218047 --
obs0.208 54457 87.1 %-
Displacement parametersBiso mean: 15.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6378 810 44 496 7728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 718 10.3 %
Rwork0.219 6240 -
obs--67.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP_NEW.PARAMDNA-RNA_NEW.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection all: 54457 / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.219

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