[English] 日本語
Yorodumi
- PDB-3ci2: REFINEMENT OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF BARLEY ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ci2
TitleREFINEMENT OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF BARLEY SERINE PROTEINASE INHIBITOR 2 AND COMPARISON WITH THE STRUCTURES IN CRYSTALS
ComponentsCHYMOTRYPSIN INHIBITOR 2
KeywordsSERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / response to wounding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodSOLUTION NMR
AuthorsPoulsen, F.M.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals.
Authors: Ludvigsen, S. / Shen, H.Y. / Kjaer, M. / Madsen, J.C. / Poulsen, F.M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Accurate Measurements of Coupling Constants from Two-Dimensional Nuclear Magnetic Resonance Spectra of Proteins and Determination of Phi-Angles
Authors: Ludvigsen, S. / Andersen, K.V. / Poulsen, F.M.
#2: Journal: J.Magn.Reson. / Year: 1990
Title: Application of Symmetry Projection Operators to Measurements of Coupling Constants in 2D NMR Spectra of Proteins
Authors: Shen, H. / Ludvigsen, S. / Poulsen, F.M.
#3: Journal: Alfred Benzon Symp. / Year: 1988
Title: The Three-Dimensional Structure of Barley Serine Proteinase Inhibitor-2 in Solution as Determined by Proton Nuclear Magnetic Resonance Spectroscopy
Authors: Poulsen, F.M. / Kjaer, M. / Clore, G.M. / Gronenborn, A.M.
#4: Journal: Protein Eng. / Year: 1987
Title: The Determination of the Three-Dimensional Structure of Barley Serine Proteinase Inhibitor 2 by Nuclear Magnetic Resonance, Distance Geometry and Restrained Molecular Dynamics
Authors: Clore, G.M. / Gronenborn, A.M. / Kjaer, M. / Poulsen, F.M.
#5: Journal: Protein Eng. / Year: 1987
Title: Comparison of the Solution and X-Ray Structures of Barley Serine Proteinase Inhibitor 2
Authors: Clore, G.M. / Gronenborn, A.M. / James, M.N.G. / Kjaer, M. / Mcphalen, C.A. / Poulsen, F.M.
#6: Journal: Carlsberg Res.Commun. / Year: 1987
Title: Secondary Structure of Barley Serine Proteinase Inhibitor 2 Determined by Proton Nuclear Magnetic Resonance Spectroscopy
Authors: Kjaer, M. / Poulsen, F.M.
#7: Journal: Carlsberg Res.Commun. / Year: 1987
Title: Sequence Specific Assignment of the Proton Nuclear Magnetic Resonance Spectrum of Barley Serine Proteinase Inhibitor 2
Authors: Kjaer, M. / Ludvigsen, S. / Sorensen, O.W. / Denys, L.A. / Kindtler, J. / Poulsen, F.M.
History
DepositionSep 10, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHYMOTRYPSIN INHIBITOR 2


Theoretical massNumber of molelcules
Total (without water)7,5481
Polymers7,5481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein CHYMOTRYPSIN INHIBITOR 2


Mass: 7547.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / References: UniProt: P01053

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

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