[English] 日本語
Yorodumi
- PDB-1xfr: Solution structure of the Bombyx mori pheromone-binding protein f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xfr
TitleSolution structure of the Bombyx mori pheromone-binding protein fragment BmPBP(1-128) at pH 6.5
ComponentsPheromone-binding protein
KeywordsTRANSPORT PROTEIN / INSECT ODORANT-BINDING PROTEIN / BOMBYX MORI PHEROMONE-BINDING PROTEIN / BMPBPB / ALPHA-HELICAL TRANSPORT PROTEIN / TRUNCATED FRAGMENT BMPBP(1-128)
Function / homology
Function and homology information


response to pheromone / pheromone binding
Similarity search - Function
Odorant/pheromone binding protein, Lepidoptera / 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
Pheromone-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION
AuthorsMichel, E. / Damberger, F.F. / Leal, W.S. / Wuthrich, K.
CitationJournal: J. Mol. Biol. / Year: 2011
Title: Dynamic conformational equilibria in the physiological function of the Bombyx mori pheromone-binding protein.
Authors: Michel, E. / Damberger, F.F. / Ishida, Y. / Fiorito, F. / Lee, D. / Leal, W.S. / Wuthrich, K.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 5, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_exptl_sample_conditions.pressure_units
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pheromone-binding protein


Theoretical massNumber of molelcules
Total (without water)14,4921
Polymers14,4921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7440 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #5closest to the average

-
Components

#1: Protein Pheromone-binding protein / PBP


Mass: 14491.513 Da / Num. of mol.: 1 / Fragment: BMPBP(1-128)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P34174
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: Two 13C-resolved NOESY spectra were used for the aliphatic and aromatic carbons respectively.

-
Sample preparation

DetailsContents: 1.1mM BmPBP(1-128) U-15N,13C; 50mM potassium phosphate buffer; 0.2% sodium azide; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 78mM / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 900 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CARA1.1R.Kellercollection
DYANA6.01T.Herrmann, P.Guntertstructure solution
DYANA6.01T.Herrmann, P.Guntertrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION / Software ordinal: 1
Details: The structure is based on 2368 NOE-derived distance constraints, and 560 dihedral angle constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 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