[English] 日本語
Yorodumi
- PDB-1c3z: THP12-CARRIER PROTEIN FROM YELLOW MEAL WORM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c3z
TitleTHP12-CARRIER PROTEIN FROM YELLOW MEAL WORM
ComponentsTHP12 CARRIER PROTEIN
KeywordsANTIFREEZE PROTEIN / EF-HAND / ALL-ALPHA
Function / homology
Function and homology information


Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
12 kDa hemolymph protein
Similarity search - Component
Biological speciesTenebrio molitor (yellow mealworm)
MethodSOLUTION NMR / MINIMIZED AVERAGE STRUCTURE OF ENSEMBLE OF 23 STRUCTURES
AuthorsSoennichsen, F.D.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: A new class of hexahelical insect proteins revealed as putative carriers of small hydrophobic ligands.
Authors: Rothemund, S. / Liou, Y.C. / Davies, P.L. / Krause, E. / Sonnichsen, F.D.
#1: Journal: Biochemistry / Year: 1997
Title: Backbone Structure and Dynamics of a Hemolymph Protein from the Mealworm Beetle Tenebrio molitor
Authors: Rothemund, S / Liou, Y.-C. / Davies, P.L. / Soennichsen, F.D.
History
DepositionJul 10, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THP12 CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,3351
Polymers12,3351
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 / -
Representative

-
Components

#1: Protein THP12 CARRIER PROTEIN


Mass: 12334.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tenebrio molitor (yellow mealworm)
Description: THIS SEQUENCE OCCURS NATURALLY IN YELLOW MEAL WORM
Plasmid: PET20B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q27011

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1314D 13C-SEPARATED NOESY
141CBCACONNH
151HN(CA)CB
161HNHA

-
Sample preparation

Details
Solution-IDContents
11MM PROTEIN, N15- OR N15/C13-DOUBLE LABELED
21MM PROTEIN, N15- OR N15/C13-DOUBLE LABELED
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1NO SALT 6.9 AMBIENT 25 K
2NO SALT 6.9 AMBIENT 25 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeSGI6X.M4DELAGLIO, F. ET AL.processing
PIPP3.6.8GARRET, D. ET AL.data analysis
X-PLOR3.81BRUENGERstructure solution
X-PLOR3.81BRUENGERrefinement
RefinementMethod: MINIMIZED AVERAGE STRUCTURE OF ENSEMBLE OF 23 STRUCTURES
Software ordinal: 1
NMR ensembleConformers 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