[English] 日本語
Yorodumi
- PDB-1skt: SOLUTION STRUCTURE OF APO N-DOMAIN OF TROPONIN C, NMR, 40 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1skt
TitleSOLUTION STRUCTURE OF APO N-DOMAIN OF TROPONIN C, NMR, 40 STRUCTURES
ComponentsTROPONIN-C
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / LOW-TEMPERATURE
Function / homology
Function and homology information


Striated Muscle Contraction / troponin complex / skeletal muscle contraction / calcium ion binding
Similarity search - Function
EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Troponin C, skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / DISGEO,SA
AuthorsTsuda, S. / Miura, A. / Gagne, S.M. / Spyracopoulos, L. / Sykes, B.D.
Citation
Journal: Biochemistry / Year: 1999
Title: Low-temperature-induced structural changes in the Apo regulatory domain of skeletal muscle troponin C.
Authors: Tsuda, S. / Miura, A. / Gagne, S.M. / Spyracopoulos, L. / Sykes, B.D.
#1: Journal: To be Published
Title: Low Temperature Effect on Dynamics of Apo N-Domain of Troponin C
Authors: Tsuda, S. / Gagne, S.M. / Spyracopoulos, L. / Sykes, B.D.
History
DepositionApr 6, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / 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_database_status.process_site / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TROPONIN-C


Theoretical massNumber of molelcules
Total (without water)9,9841
Polymers9,9841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100LEAST RESTRAINT VIOLATION
Representative

-
Components

#1: Protein TROPONIN-C / NTNC APO


Mass: 9984.085 Da / Num. of mol.: 1 / Fragment: N-DOMAIN, RESIDUES 1-90
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-90 OF CHICKEN SKELETAL MUSCLE TROPONIN C IN CA2+-FREE STATE
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: SKELETON / Gene: NTNC / Organ: SKELETAL / Plasmid: PET3A / Gene (production host): NTNC / Production host: Escherichia coli (E. coli) / References: UniProt: P02588

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCACONNH
12115N-NOESY
131HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C,15N-LABELED APO NTNC.

-
Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: 50mM KCL / pH: 6.7 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY500VarianUNITY5005001
Varian 600Varian6006002

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NMRPipestructure solution
PIPPstructure solution
RefinementMethod: DISGEO,SA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 40

+
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