[English] 日本語
Yorodumi
- SASDBK3: Bovine serum albumin, dimer from SEC-SAXS (Bovine serum albumin, ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: SASBDB / ID: SASDBK3
SampleBovine serum albumin, dimer from SEC-SAXS
Bovine serum albumin, dimer (protein), BSA dimer, Bos taurus
SourceBos taurus / mammal / ウシ /
Citation

Nat Protoc, 2016 Nov, 11, 2122-2153
Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.
Jeffries CM / Graewert MA / Blanchet CE / Langley DB / Whitten AE

Contact authorDmitri Svergun Melissa Clement Blanchet Cy M

-
Structure visualization

3D viewer


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

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

Downloads & links

-
Models

Model #448
Type: atomic / Software: CRYSOL / Radius of dummy atoms: 1.90 A / Chi-square value: 1.044
Search similar-shape structures of this assembly by Omokage search (details)
Model #450
Type: dummy / Software: DAMMIF / Radius of dummy atoms: 3.60 A / Chi-square value: 1.104601 / P-value: 0.339000
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Bovine serum albumin, dimer from SEC-SAXS
BufferName: Tris / Concentration: 25 / Unit: mM / pH: 7.5 / Composition: 150 mM NaCl 3% v/v glycerol
Entity #299Type: protein / Description: Bovine serum albumin, dimer / Formula weight: 66.462 / Number of molecules: 2 / Source: Bos taurus / References: UniProt: P02769
Sequence:
DTHKSEIAHR FKDLGEEHFK GLVLIAFSQY LQQCPFDEHV KLVNELTEFA KTCVADESHA GCEKSLHTLF GDELCKVASL RETYGDMADC CEKQEPERNE CFLSHKDDSP DLPKLKPDPN TLCDEFKADE KKFWGKYLYE IARRHPYFYA PELLYYANKY NGVFQECCQA EDKGACLLPK IETMREKVLT SSARQRLRCA SIQKFGERAL KAWSVARLSQ KFPKAEFVEV TKLVTDLTKV HKECCHGDLL ECADDRADLA KYICDNQDTI SSKLKECCDK PLLEKSHCIA EVEKDAIPEN LPPLTADFAE DKDVCKNYQE AKDAFLGSFL YEYSRRHPEY AVSVLLRLAK EYEATLEECC AKDDPHACYS TVFDKLKHLV DEPQNLIKQN CDQFEKLGEY GFQNALIVRY TRKVPQVSTP TLVEVSRSLG KVGTRCCTKP ESERMPCTED YLSLILNRLC VLHEKTPVSE KVTKCCTESL VNRRPCFSAL TPDETYVPKA FDEKLFTFHA DICTLPDTEK QIKKQTALVE LLKHKPKATE EQLKTVMENF VAFVDKCCAA DDKEACFAVE GPKLVVSTQT ALA

-
Experimental information

BeamInstrument name: PETRA III P12 / Instrument city: Hamburg / Instrument country: Germany / Type of source: X-ray synchrotron / Radiation wavelength: 0.12 / Dist spec to detc: 3.1
ScanTitle: Bovine serum albumin, dimer / Measurement date: Jan 23, 2014 / Storage temperature: 2 / Exposure time: 1 / Number of frames: 3600 / Unit: 1/nm / Qmin: 0.0779 / Qmax: 3.4555
Distance distribution function P(R)Software p of R: GNOM 4.6 / Number of points: 427 / Qmin: 0.07526 / Qmax: 3.441 / P of R point min: 21 / P of R point max: 447 / Rmin: 0 / Rmax: 12.71
ResultSASBDB code: SASDBK3 / Experimental MW: 133.6 / MW Porod: 125.9 / I0 from PR: 219.7 / I0 from PR error: 1.26 / I0 from Guinier: 217.8 / I0 from Guinier error: 1.32 / Rg from PR: 4.02 / Rg from PR error: 0.03 / Rg from Guinier: 3.89 / Rg from Guinier error: 0.06 / D max: 12.7 / Porod volume: 201.5 / Guinier point min: 1 / Guinier point max: 98 / Type of curve: other

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
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)

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