[English] 日本語
Yorodumi
- SASDFR7: Rabbit muscle fructose-bisphosphate aldolase A, K229M mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFR7
SampleRabbit muscle fructose-bisphosphate aldolase A, K229M mutant
  • Fructose-bisphosphate aldolase A (protein), Aldolase, Oryctolagus cuniculus
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / I band / M band / glycolytic process / protein homotetramerization / positive regulation of cell migration
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Contact author
  • Normand Cyr (Département de biochimie, Université de Montréal, Montréal, Canada)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #3194
Type: atomic / Symmetry: P222 / Chi-square value: 1.659 / P-value: 0.000021
Model #3193
Type: dummy / Radius of dummy atoms: 3.50 A / Symmetry: P1 / Chi-square value: 1.178 / P-value: 0.008512

-
Sample

SampleName: Rabbit muscle fructose-bisphosphate aldolase A, K229M mutant
Specimen concentration: 8.66 mg/ml
BufferName: 20 mM HEPES / pH: 7
Entity #1735Name: Aldolase / Type: protein / Description: Fructose-bisphosphate aldolase A / Formula weight: 39.214 / Num. of mol.: 4 / Source: Oryctolagus cuniculus / References: UniProt: P00883
Sequence: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADDG RPFPQVIKSK GGVVGIKVDK GVVPLAGTNG ETTTQGLDGL SERCAQYKKD GADFAKWRCV LKIGEHTPSA LAIMENANVL ...Sequence:
PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADDG RPFPQVIKSK GGVVGIKVDK GVVPLAGTNG ETTTQGLDGL SERCAQYKKD GADFAKWRCV LKIGEHTPSA LAIMENANVL ARYASICQQN GIVPIVEPEI LPDGDHDLKR CQYVTEKVLA AVYKALSDHH IYLEGTLLMP NMVTPGHACT QKYSHEEIAM ATVTALRRTV PPAVTGVTFL SGGQSEEEAS INLNAINKCP LLKPWALTFS YGRALQASAL KAWGGKKENL KAAQEEYVKR ALANSLACQG KYTPSGQAGA AASESLFISN HAY

-
Experimental information

BeamInstrument name: Université de Montréal Xenocs BioXolver L with MetalJet
City: Montréal / 国: Canada / Type of source: X-ray in house / Wavelength: 1.348 Å / Dist. spec. to detc.: 600 mm
DetectorName: Pilatus3 R 300K / Pixsize x: 172 mm
Scan
Title: Rabbit muscle fructose-bisphosphate aldolase A, K229M mutant
Measurement date: Jun 14, 2019 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 60 sec. / Number of frames: 10 / Unit: 1/A /
MinMax
Q0.0107 0.3999
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 429 /
MinMax
Q0.0106922 0.579347
P(R) point1 429
R0 118
Result
Type of curve: single_conc
ExperimentalStandardPorod
MW157.3 kDa160 kDa133 kDa
Volume--213 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.1303 0.0002174 0.1302 0.0002708
Radius of gyration, Rg3.6 nm0.007 3.602 nm0.011

MinMax
D-11.8
Guinier point1 20

+
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