[English] 日本語
Yorodumi
- SASDBJ7: Pomacea maculata perivitellin 1 (PmPV1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDBJ7
SamplePomacea maculata perivitellin 1
  • Pomacea maculata perivitellin 1 (protein), PmPV1, Pomacea maculata (Perry, 1810)
Biological speciesPomacea maculata (Perry
1810)
CitationDate: 2017 Dec
Title: Convergent evolution of plant and animal embryo defences by hyperstable non-digestible storage proteins
Authors: Pasquevich M / Dreon M / Qiu J / Mu H
Contact author
  • Marcos Dreon

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #815
Type: dummy / Radius of dummy atoms: 3.00 A / Chi-square value: 11.066
Search similar-shape structures of this assembly by Omokage search (details)
Model #816
Type: dummy / Radius of dummy atoms: 3.00 A / Chi-square value: 11.134
Search similar-shape structures of this assembly by Omokage search (details)
Model #817
Type: dummy / Radius of dummy atoms: 3.00 A / Chi-square value: 11.318
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Pomacea maculata perivitellin 1 / Specimen concentration: 1.37-0.66
BufferName: 100 mM Phosphate Buffer / pH: 7.4
Entity #458Name: PmPV1 / Type: protein / Description: Pomacea maculata perivitellin 1 / Formula weight: 23.184 / Num. of mol.: 12 / Source: Pomacea maculata (Perry, 1810)
Sequence: MAATLVLLLA MSTLLTSGVE MIKHDLVFLE VDSGSCKENA SKIFQDKSMI PGEVSGQVIG TSKFFAVLRE QDLARMNLKD VKEVVPVTKL EDYLESWNAS WRIHRDINET DLWLFKVSPN PKSKTLQQYD NQVRHGVRIA APVMENFPNY ILLSKGVFPP KYYIFINKKE ...Sequence:
MAATLVLLLA MSTLLTSGVE MIKHDLVFLE VDSGSCKENA SKIFQDKSMI PGEVSGQVIG TSKFFAVLRE QDLARMNLKD VKEVVPVTKL EDYLESWNAS WRIHRDINET DLWLFKVSPN PKSKTLQQYD NQVRHGVRIA APVMENFPNY ILLSKGVFPP KYYIFINKKE EFPKDFRNIL DIFGGPGAVK VESLYVRILI SWQ

-
Experimental information

BeamInstrument name: Brazilian Synchrotron Light Laboratory SAXS2 Beamline
City: Campinas / 国: Brazil / Type of source: X-ray synchrotron / Wavelength: 1.55 Å / Dist. spec. to detc.: 1.51154 mm
DetectorName: MAR 165 CCD
Scan
Title: Pomacea maculata perivitellin 1 / Measurement date: Mar 26, 2015 / Cell temperature: 25 °C / Exposure time: 300 sec. / Number of frames: 5 / Unit: 1/nm /
MinMax
Q0.0974 2.1123
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 208 /
MinMax
Q0.1649 1.91
P(R) point9 216
R0 14.32
Result
Type of curve: single_conc /
ExperimentalPorod
MW294 kDa335 kDa
Volume-537 nm3

P(R)GuinierGuinier errorP(R) error
Forward scattering, I00.001938 0.0019 2.0E-5 -
Radius of gyration, Rg4.26 nm4.18 nm0.07 0.002

MinMax
D-14.32
Guinier point3 28

+
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://pdbjlvh1.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