[English] 日本語
Yorodumi
- PDB-1fmy: HIGH RESOLUTION SOLUTION STRUCTURE OF THE PROTEIN PART OF CU7 MET... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fmy
TitleHIGH RESOLUTION SOLUTION STRUCTURE OF THE PROTEIN PART OF CU7 METALLOTHIONEIN
ComponentsMETALLOTHIONEIN
KeywordsMETAL BINDING PROTEIN / metallothionein / copper / Saccharomyces cerevisiae
Function / homology
Function and homology information


detoxification of cadmium ion / detoxification of copper ion / response to copper ion / superoxide dismutase activity / cadmium ion binding / antioxidant activity / removal of superoxide radicals / copper ion binding / cytosol
Similarity search - Function
Ag-metallothionein / Metallothionein domain superfamily, yeast / Metallothionein domain, yeast / Copper metallothionein superfamily / Yeast metallothionein / Metallothionein domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Copper metallothionein 1-1 / Copper metallothionein 1-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry simulated annealing torsion angle dynamics
Model type detailsminimized average
AuthorsBertini, I. / Hartmann, H.J. / Klein, T. / Liu, G. / Luchinat, C. / Weser, U.
CitationJournal: Eur.J.Biochem. / Year: 2000
Title: High resolution solution structure of the protein part of Cu7 metallothionein.
Authors: Bertini, I. / Hartmann, H.J. / Klein, T. / Liu, G. / Luchinat, C. / Weser, U.
History
DepositionAug 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METALLOTHIONEIN


Theoretical massNumber of molelcules
Total (without water)4,2761
Polymers4,2761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 30mean structure
RepresentativeModel #1minimized average structure

-
Components

#1: Protein/peptide METALLOTHIONEIN /


Mass: 4275.656 Da / Num. of mol.: 1 / Fragment: RESIDUES 9 TO 48 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: X-2180-1AA / References: UniProt: P07215, UniProt: P0CX80*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
2312D NOESY
2412D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 5mM unenrich metallothionein; 18mM phosphate buffer; 90% H2O, 10% D2O;pH=6.5; 0.03% beta-mercaptoethanol
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.02 6.5 normal 283 K
20.02 6.5 normal 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerdata analysis
XwinNMR3.1Brukerprocessing
DYANA1.5Guntert, P. ,et. alstructure solution
Amber5Pearlman, D. A., et. alrefinement
XEASY3.1Eccles, C., et.al.data analysis
RefinementMethod: distance geometry simulated annealing torsion angle dynamics
Software ordinal: 1
Details: A total of 1192 NOES, of which 1048 are meaningful, were used to determine the solution structure.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: mean structure / Conformers calculated total number: 30 / Conformers submitted total number: 1

+
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