[English] 日本語
Yorodumi
- PDB-2y7c: Atomic model of the Ocr-bound methylase complex from the Type I r... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2y7c
TitleAtomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
DescriptorTYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
GENE 0.3 PROTEIN
KeywordsTRANSFERASE
Specimen sourceENTEROBACTERIA PHAGE T7 / virus
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (18 A resolution / Single particle / Negative stain)
AuthorsKennaway, C.K. / Obarska-Kosinska, A. / White, J.H. / Tuszynska, I. / Cooper, L.P. / Bujnicki, J.M. / Trinick, J. / Dryden, D.T.F.
CitationNucleic Acids Res., 2009, 37, 762-770

Nucleic Acids Res., 2009, 37, 762-770 StrPapers
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
Christopher K Kennaway / Agnieszka Obarska-Kosinska / John H White / Irina Tuszynska / Laurie P Cooper / Janusz M Bujnicki / John Trinick / David T F Dryden

DateDeposition: Jan 31, 2011 / Release: Feb 9, 2011 / Last modification: Mar 20, 2013

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
B: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
C: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
D: GENE 0.3 PROTEIN
E: GENE 0.3 PROTEIN


Theoretical massNumber of molelcules
Total (without water)197,6075
Polyers197,6075
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Polypeptide(L)TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT / S.ECOKI / TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / S PROTEIN


Mass: 51468.723 Da / Num. of mol.: 1
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P05719, EC: 3.1.21.3

Molecular function

Biological process

#2: Polypeptide(L)TYPE I RESTRICTION ENZYME ECOKI M PROTEIN / HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT / M.ECOKI


Mass: 59378.996 Da / Num. of mol.: 2
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P08957, EC: 3.1.21.3, EC: 2.1.1.72

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)GENE 0.3 PROTEIN / OCR ANTIRESTRICTION PROTEIN / DNA MIMIC


Mass: 13690.008 Da / Num. of mol.: 2 / Source: (gene. exp.) ENTEROBACTERIA PHAGE T7 / virus / References: UniProt: P03775

Biological process

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: NEGATIVE STAIN

-
Sample preparation

Assembly of specimenName: M.ECOKI WITH OCR / Aggregation state: PARTICLE
Buffer solutionName: 20MM TRIS-CL, 100 MM NACL
Sample preparationpH: 4.7 / Sample conc.: 0.05 mg/ml
Specimen supportDetails: CARBON

-
Electron microscopy imaging

MicroscopyMicroscope model: OTHER / Date: Feb 1, 2008
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 25 e/A2 / Illumination mode: MEDIUM DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 39500 X / Nominal defocus max: 870 nm / Nominal defocus min: 275 nm / Cs: 2 mm
Specimen holderTemperature: 294 K
CameraType: KODAK SO163 FILM
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: IMAGIC, EMAN, MRC,UROX,CHIMERA / Number of particles: 17807
3D reconstructionResolution: 18 A / Nominal pixel size: 3.12 A/pix / Actual pixel size: 3.12 A/pix / Magnification calibration: TMV / CTF correction method: FILTERED AT FIRST ZERO
Details: HSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY.
Atomic model buildingMethod: UROX / Ref protocol: RIGID BODY / Ref space: REAL
Atomic model buildingPDB-ID: 1S7Z, 1YF2, 2AR0
Least-squares processHighest resolution: 18 A
Refine hist #LASTHighest resolution: 18 A
Number of atoms included #LASTProtein: 13725 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 13725

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more