[English] 日本語
Yorodumi
- SASDFL6: Adenine specific DNA methyltransferase (Mod Hp_0593) at pH 8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFL6
SampleAdenine specific DNA methyltransferase (Mod Hp_0593) at pH 8
  • Adenine specific DNA methyltransferase (Mod) (protein), Helicobacter pylori (strain ATCC 700392 / 26695)
Function / homology
Function and homology information


macromolecule modification / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / methyltransferase activity / methylation / DNA binding / cytoplasm
Similarity search - Function
N4/N6-methyltransferase, Type III restriction-modification enzyme EcoPI Mod subunit-like / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Adenine specific DNA methyltransferase (Mod)
Similarity search - Component
Biological speciesHelicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Contact author
  • Naveen Narayanan (RCB, Regional Centre for Biotechnology, Haryana, India)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3043
Type: atomic / Chi-square value: 1.219
Search similar-shape structures of this assembly by Omokage search (details)
Model #3044
Type: atomic / Chi-square value: 2.085
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Adenine specific DNA methyltransferase (Mod Hp_0593) at pH 8
Specimen concentration: 2 mg/ml
BufferName: 25 mM Tris, 250 mM NaCl / pH: 8
Entity #1674Type: protein / Description: Adenine specific DNA methyltransferase (Mod) / Formula weight: 68.3 / Num. of mol.: 2 / Source: Helicobacter pylori (strain ATCC 700392 / 26695) / References: UniProt: O25315
Sequence: MLLKNFPQTI KDGQVSLSAI KMLLGFNESM NDISGYELTW TGKGFANALY SEPCQKQLKL QESFTPQTSA SKHPNNAIII GDNLDALKLL KSAYSEKIKM IYIDPPYNTG NDEFIYPDNF RQDYQKILRE VGLMEIDENG KEIESESLKF FKNTQGSGTH SGWLSFMLPR ...Sequence:
MLLKNFPQTI KDGQVSLSAI KMLLGFNESM NDISGYELTW TGKGFANALY SEPCQKQLKL QESFTPQTSA SKHPNNAIII GDNLDALKLL KSAYSEKIKM IYIDPPYNTG NDEFIYPDNF RQDYQKILRE VGLMEIDENG KEIESESLKF FKNTQGSGTH SGWLSFMLPR LKLARDLLKE DGVIFISIDD NECANLKILC DEIFGEDNFV GDFIRKTKST TNDAKIGLNY QHEFLLCYAK DKNYTNLLGG EKNLENYKNP DNDPNGAWIN DNPSAKSGNM KTGYFGVTNP YTNKVDYPPV GMFWRFSQNT IQKHIDEGRI CFKKEHKDNE RGFIYKRYLK DLKTTQKTFD SLIFSDNCYM NQAATKELLN LGMGEYFTYP KGVEFMKKII LHSTTPNEGD IILDFFAGSG TTVHAVMELN AEDKGNREFI LVQIDEEIKE DESAYDFCKK ELKSAKPVIS DITIERVKRA AQKISQLSKD SGLDLGFKVY TLQDKVQIIN DKEEITLFNR SDLTPFDKAL NLALQCGKTL NQALEIIIKD KLYKCEDAYF CIVCDEEAQE YLAKSKNEMI FLDGYEEIDL EAFLNLNASF KERLSVVY

-
Experimental information

BeamInstrument name: ESRF ID14-3 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.0992 Å
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Adenine specific DNA methyltransferase (Mod), Hp_0593, pH 8
Measurement date: Jul 9, 2017 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.5 sec. / Number of frames: 10 / Unit: 1/nm /
MinMax
Q0.0355 4.9391
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 581 /
MinMax
Q0.172928 2.92082
P(R) point1 581
R0 12.5
Result
Type of curve: single_conc /
ExperimentalPorod
MW120 kDa90 kDa
Volume-143 nm3

P(R)GuinierGuinier error
Forward scattering, I035.98 35.57 0.086
Radius of gyration, Rg3.375 nm3.27 nm0.74

MinMax
D-12.5
Guinier point30 77

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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