[English] 日本語
Yorodumi
- PDB-1cir: COMPLEX OF TWO FRAGMENTS OF CI2 [(1-40)(DOT)(41-64)] -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cir
TitleCOMPLEX OF TWO FRAGMENTS OF CI2 [(1-40)(DOT)(41-64)]
Components(CHYMOTRYPSIN INHIBITOR 2) x 2
KeywordsSERINE PROTEASE INHIBITOR
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Subtilisin-chymotrypsin inhibitor-2A
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodSOLUTION NMR
AuthorsDavis, B.J. / Fersht, A.R.
Citation
Journal: Structure Fold.Des. / Year: 1996
Title: Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary ...Title: Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary fragments of cleaved chymotrypsin inhibitor 2. Direct evidence for a nucleation-condensation mechanism
Authors: Neira, J.L. / Davis, B. / Ladurner, A.G. / Buckle, A.M. / Gay Gde, P. / Fersht, A.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The Structure of the Transition State for the Association of Two Fragments of the Barley Chymotrypsin Inhibitor-2 to Generate Native-Like Protein: Implications for Mechanisms of Protein Folding
Authors: De Prat Gay, G. / Ruiz-Sanz, J. / Davis, B. / Fersht, A.R.
#2: Journal: Biochemistry / Year: 1994
Title: Generation of a Family of Protein Fragments for Structure-Folding Studies. 1. Folding Complementation of Two Fragments of Chymotrypsin Inhibitor-2 Formed by Cleavage at its Unique Methionine Residue
Authors: De Prat Gay, G. / Fersht, A.R.
History
DepositionOct 2, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: CHYMOTRYPSIN INHIBITOR 2
B: CHYMOTRYPSIN INHIBITOR 2


Theoretical massNumber of molelcules
Total (without water)7,3022
Polymers7,3022
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 / -
Representative

-
Components

#1: Protein/peptide CHYMOTRYPSIN INHIBITOR 2 / CI2


Mass: 4424.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLEAVED BETWEEN RESIDUES 40 AND 41 / Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: PTZ18U / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
#2: Protein/peptide CHYMOTRYPSIN INHIBITOR 2 / CI2


Mass: 2877.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLEAVED BETWEEN RESIDUES 40 AND 41 / Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: PTZ18U / Production host: Escherichia coli (E. coli) / References: UniProt: P01053

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers 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