[English] 日本語
- SASDAN2: RNase in PBS (Ribonuclease pancreatic, RNase) -

Open data

ID or keywords:


no data

Basic information

Database: SASBDB / ID: SASDAN2
SampleRNase in PBS
Ribonuclease pancreatic (protein), RNase, Bos taurus
SourceBos taurus / mammal / Cattle (Wikipedia) /
Contact authorDarja Ruskule (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Structure visualization

3D viewer

Downloads & links


Model #25
Type: dummy / Software: gasbor / Radius of dummy atoms: 1.90 A / Symmetry: P1
Comment: Gasbori run 10 times, damsel identified structure with lowest NSD
Chi-square value: 2.4025
Search similar-shape structures of this assembly by Omokage search (details)
Model #24
Type: atomic / Software: CRYSOL_30 / Symmetry: P1 / Chi-square value: 1.493284
Search similar-shape structures of this assembly by Omokage search (details)


SampleName: RNase in PBS / Ext coefficient: 6.9 / Contrast: 3.163 / Specific vol: 0.7279 / Purity method: gel filtration / Dry vol: 19917 / Sample MW: 16.46 / Specimen concentration: 22.6 / Concentration method: nanodrop
BufferName: PBS / PK: 7 / pH: 7.4
Entity #17Type: protein / Description: Ribonuclease pancreatic / Formula weight: 16.46 / Number of molecules: 1 / Source: Bos taurus / References: UniProt: P61823

Experimental information

BeamInstrument name: DORIS III X33 / Instrument city: Hamburg / Instrument country: Germany / Shape: 0.6 / Type of source: X-ray synchrotron / Radiation wavelength: 0.15 / Dist spec to detc: 2.7
ScanTitle: WAXS / Measurement date: Sep 18, 2012 / Storage temperature: 1 / Cell temperature: 1 / Exposure time: 15 / Number of frames: 8 / Unit: 1/nm / Qmin: 0.0871 / Qmax: 17.6809
Distance distribution function P(R)Software p of R: GNOM 5.0 / Number of points: 801 / Qmin: 0.6312 / Qmax: 2.82117 / P of R point min: 1 / P of R point max: 801 / Rmin: 0 / Rmax: 5
ResultSASBDB code: SASDAN2 / Experimental MW: 14.5 / MW standard: 14.5 / I0 from PR: 13.4 / I0 from Guinier: 13.5 / Rg from PR: 1.59 / Rg from Guinier: 1.58 / D max: 5 / Porod volume: 14.7 / Guinier point min: 136 / Guinier point max: 271 / Type of curve: merged / Standard: BSA / Comments: merged

About Yorodumi


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


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