[English] 日本語
Yorodumi
- PDB-1aqi: STRUCTURE OF ADENINE-N6-DNA-METHYLTRANSFERASE TAQI -

+
Open data


ID or keywords:

Loading...

-
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
Restriction modification methylase Eco57I / Eco57I restriction-modification methylase / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / N6 adenine-specific DNA methyltransferase, TaqI class / Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / 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 ...Restriction modification methylase Eco57I / Eco57I restriction-modification methylase / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / N6 adenine-specific DNA methyltransferase, TaqI class / Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Modification methylase 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, 1996-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
γ
α
β
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more