[English] 日本語
Yorodumi
- SASDAA2: Conalbumin in PBS (Ovotransferrin) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDAA2
SampleConalbumin in PBSOvotransferrin
  • Ovotransferrin (protein), Gallus gallus
Function / homology
Function and homology information


extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / antibacterial humoral response / iron ion transport / response to lipopolysaccharide ...extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / antibacterial humoral response / iron ion transport / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / plasma membrane
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Contact author
  • Darja Ruskule (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #14
Type: dummy / Software: dammif / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.034289
Search similar-shape structures of this assembly by Omokage search (details)
Model #13
Type: atomic / Software: crysol (28) / Chi-square value: 3.404025
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Conalbumin in PBSOvotransferrin / Ext coefficient: 11.63 / Purity method: gel filtration / Dry vol: 99221 / Sample MW: 311.12 kDa / Specimen concentration: 12.17 mg/ml / Concentration method: nanodrop
BufferName: PBS / PK: 7 / pH: 7.4
Entity #12Type: protein / Description: Ovotransferrin / Formula weight: 77.78 / Num. of mol.: 1 / Source: Gallus gallus / References: UniProt: P02789
Sequence: MKLILCTVLS LGIAAVCFAA PPKSVIRWCT ISSPEEKKCN NLRDLTQQER ISLTCVQKAT YLDCIKAIAN NEADAISLDG GQAFEAGLAP YKLKPIAAEV YEHTEGSTTS YYAVAVVKKG TEFTVNDLQG KTSCHTGLGR SAGWNIPIGT LLHRGAIEWE GIESGSVEQA ...Sequence:
MKLILCTVLS LGIAAVCFAA PPKSVIRWCT ISSPEEKKCN NLRDLTQQER ISLTCVQKAT YLDCIKAIAN NEADAISLDG GQAFEAGLAP YKLKPIAAEV YEHTEGSTTS YYAVAVVKKG TEFTVNDLQG KTSCHTGLGR SAGWNIPIGT LLHRGAIEWE GIESGSVEQA VAKFFSASCV PGATIEQKLC RQCKGDPKTK CARNAPYSGY SGAFHCLKDG KGDVAFVKHT TVNENAPDQK DEYELLCLDG SRQPVDNYKT CNWARVAAHA VVARDDNKVE DIWSFLSKAQ SDFGVDTKSD FHLFGPPGKK DPVLKDLLFK DSAIMLKRVP SLMDSQLYLG FEYYSAIQSM RKDQLTPSPR ENRIQWCAVG KDEKSKCDRW SVVSNGDVEC TVVDETKDCI IKIMKGEADA VALDGGLVYT AGVCGLVPVM AERYDDESQC SKTDERPASY FAVAVARKDS NVNWNNLKGK KSCHTAVGRT AGWVIPMGLI HNRTGTCNFD EYFSEGCAPG SPPNSRLCQL CQGSGGIPPE KCVASSHEKY FGYTGALRCL VEKGDVAFIQ HSTVEENTGG KNKADWAKNL QMDDFELLCT DGRRANVMDY RECNLAEVPT HAVVVRPEKA NKIRDLLERQ EKRFGVNGSE KSKFMMFESQ NKDLLFKDLT KCLFKVREGT TYKEFLGDKF YTVISSLKTC NPSDILQMCS FLEGK

-
Experimental information

BeamInstrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
DetectorName: Pilatus 1M-W / Pixsize x: 0.172 mm
Scan
Measurement date: Sep 21, 2012 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 15 sec. / Number of frames: 8 / Unit: 1/nm /
MinMax
Q0.0871 6.0145
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1224 /
MinMax
Q0.294912 3.64138
P(R) point1 1224
R0 11
Result
Type of curve: merged / Standard: BSA /
ExperimentalStandardPorod
MW68 kDa68 kDa-
Volume--116.6 nm3

P(R)Guinier
Forward scattering, I070 82.8
Radius of gyration, Rg3.36 nm3.78 nm

MinMax
D-11
Guinier point38 95

+
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