[English] 日本語
Yorodumi
- SASDF99: Bovine serum albumin monomer - SEC-SAXS/WAXS coupled to multiangl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDF99
SampleBovine serum albumin monomer - SEC-SAXS/WAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)
  • Bovine serum albumin (protein), BSA, Bos taurus
Function / homology
Function and homology information


enterobactin binding / cellular response to calcium ion starvation / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...enterobactin binding / cellular response to calcium ion starvation / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
Contact author
  • Melissa Graewert
  • Cy M Jeffries

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3558
Type: dummy / Software: (2.3i) / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.45 / P-value: 0.298705
Search similar-shape structures of this assembly by Omokage search (details)
Model #3560
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 2.417
Search similar-shape structures of this assembly by Omokage search (details)
Model #3559
Type: atomic / Symmetry: P1 / Chi-square value: 1.548 / P-value: 0.033334
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Bovine serum albumin monomer - SEC-SAXS/WAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)
Specimen concentration: 15 mg/ml
BufferName: 50 mM HEPES, 3% v/v glycerol, / pH: 7.5
Entity #1306Name: BSA / Type: protein / Description: Bovine serum albumin / Formula weight: 66.432 / Num. of mol.: 1 / Source: Bos taurus / References: UniProt: P02769
Sequence: DTHKSEIAHR FKDLGEEHFK GLVLIAFSQY LQQCPFDEHV KLVNELTEFA KTCVADESHA GCEKSLHTLF GDELCKVASL RETYGDMADC CEKQEPERNE CFLSHKDDSP DLPKLKPDPN TLCDEFKADE KKFWGKYLYE IARRHPYFYA PELLYYANKY NGVFQECCQA ...Sequence:
DTHKSEIAHR FKDLGEEHFK GLVLIAFSQY LQQCPFDEHV KLVNELTEFA KTCVADESHA GCEKSLHTLF GDELCKVASL RETYGDMADC CEKQEPERNE CFLSHKDDSP DLPKLKPDPN TLCDEFKADE KKFWGKYLYE IARRHPYFYA PELLYYANKY NGVFQECCQA EDKGACLLPK IETMREKVLA 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 EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 1 mm
DetectorName: Pilatus 2M
Scan
Title: Bovine serum albumin monomer - SEC-SAXS/WAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)
Measurement date: Apr 23, 2017 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 63 / Unit: 1/nm /
MinMax
Q0.0827 19.5502
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 369 /
MinMax
Q0.0932055 3.97617
P(R) point1 369
R0 8.25
Result
Type of curve: sec
Comments: Protein powder (Sigma) consisting of BSA monomers, dimers, trimers and higher MW species was dissolved in the SEC-running buffer and then 0.22 micon spin filtered prior to injection onto ...Comments: Protein powder (Sigma) consisting of BSA monomers, dimers, trimers and higher MW species was dissolved in the SEC-running buffer and then 0.22 micon spin filtered prior to injection onto the SEC column. The sample injection concentration was determined from triplicate UV A280 measurements using an E0.1% of 0.646 (= 1 g/l) calculated from the amino acid sequence (ProtParam). The Rg-correlation through the SEC-SAXS/WAXS peak, the individual unsubtracted SEC-SAXS/WAXS frames as well as the results from coupled MALLS and QELS analysis are included in the full entry zip archive. The quoted experimental molecular weight was determined from the separated monomer peak using MALLS in combination with refractive-index (RI) measurements from the same sample eluting from the column using a split-flow SEC-SAXS/WAXS-light scattering configuration (Graewert et al., (2015) Sci. Reports. 5, 10734: doi: 10.1038/srep10734). The average hydrodynamic radius of the separated monomer was evaluated at 3.4 nm. Two atomistic representations of the protein are displayed: 1) The X-ray crystallography model fit to the SAXS data (PDB:4F5S), middle, and; 2) The same model after normal mode analysis/refinement using SREFLEX (bottom; Panjkovich et al., (2016) Phys. Chem. Chem. Phys. 18(8):5707-5719. doi: 10.1039/c5cp04540a). The complete SREFLEX result summary is included in the full-entry zip archive.
ExperimentalPorod
MW62.7 kDa60 kDa
Volume-95 nm3

P(R)GuinierGuinier error
Forward scattering, I04496 4502.3 2.79
Radius of gyration, Rg2.764 nm2.79 nm-

MinMax
D-8.25
Guinier point1 37

+
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