[English] 日本語
Yorodumi
- PDB-1jbn: Solution structure of an acyclic permutant of SFTI-1, A trypsin i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jbn
TitleSolution structure of an acyclic permutant of SFTI-1, A trypsin inhibitor from sunflower seeds
ComponentsCYCLIC TRYPSIN INHIBITOR
KeywordsPROTEIN BINDING / beta sheet / 1 disulfide bridge / linear backbone / 14/1-LSFTI-1
Function / homologynegative regulation of endopeptidase activity / endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / protease binding / acyclic trypsin inhibitor / Trypsin inhibitor 1
Function and homology information
Biological speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / simulated annealing, refinement with modified CSDX force field
AuthorsKorsinczky, M.L.J. / Schirra, H.J. / Rosengren, K.J. / West, J. / Condie, B.A. / Otvos, L. / Anderson, M.A. / Craik, D.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structures by 1H NMR of the novel cyclic trypsin inhibitor SFTI-1 from sunflower seeds and an acyclic permutant.
Authors: Korsinczky, M.L. / Schirra, H.J. / Rosengren, K.J. / West, J. / Condie, B.A. / Otvos, L. / Anderson, M.A. / Craik, D.J.
History
DepositionJun 6, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 13, 2016Group: Other
Revision 1.4Dec 28, 2016Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYCLIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)1,5361
Polymers1,5361
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)20 / 50structures with the least restraint violations,structures with the lowest energy
Representative

-
Components

#1: Protein/peptide CYCLIC TRYPSIN INHIBITOR / SFTI-1


Type: Polypeptide / Class: Trypsin inhibitor / Mass: 1535.829 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: acircular permutation of a naturally occurring circular peptide from sunflower seeds.
Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, acyclic trypsin inhibitor

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1332D NOESY
143E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM 14/1-lSFTI-120mM sodium phosphate, pH4.5, 20% trifluoroethanol, 10%D2O
21mM 14/1-lSFTI-120mM sodium phosphate, pH4.5, 10%D2O
31mM 14/1-lSFTI-120mM sodium phosphate, pH4.5, 20% trifluoroethanol, 80%D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM 4.5 ambient 273 K
220mM 4.5 ambient 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker ARXBrukerARX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XWINNMR2.6Brukercollection
XWINNMR2.6Brukerprocessing
ccnmrCieslar et al.data analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing, refinement with modified CSDX force field
Software ordinal: 1
Details: 162 distance constraints, 73 sequential, 18 medium range, 68 long range, 6 chi1 angle constraints, 7 phi angle constraints
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / 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://pdbjlvh1.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