[English] 日本語
Yorodumi
- PDB-1ytp: Solution structure of the C4A/C41A variant of the Nicotiana alata... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ytp
TitleSolution structure of the C4A/C41A variant of the Nicotiana alata proteinase inhibitor T1
Componentsproteinase inhibitor
KeywordsHYDROLASE INHIBITOR / beta-sheet / potII inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Proteinase inhibitor I20 / : / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Proteinase inhibitor
Similarity search - Component
Biological speciesNicotiana alata (Persian tobacco)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, explicit inclusion of water molecules (Linge, Nilges, 1999)
AuthorsSchirra, H.J. / Renda, R.R. / Anderson, M.A. / Craik, D.J.
CitationJournal: TO BE PUBLISHED
Title: The structure of a disulfide mutant of the Nicotiana alata proteinase inhibitor T1 --- Stabilisation of the reactive site loop is critical for activity
Authors: Schirra, H.J. / Renda, R.R. / Anderson, M.A. / Craik, D.J.
History
DepositionFeb 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)5,6761
Polymers5,6761
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 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #11lowest energy

-
Components

#1: Protein proteinase inhibitor


Mass: 5676.383 Da / Num. of mol.: 1 / Fragment: residues 1-53 / Mutation: C4A, C41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana alata (Persian tobacco) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: GenBank: 473591, UniProt: Q40378*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM C4A/C41A-T190% H2O/10% D2O
21mM C4A/C41A-T199% D2O
Sample conditionsIonic strength: 1mM / pH: 5.8 / Pressure: ambient / Temperature: 313 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX5001
Bruker DMXBrukerDMX7502

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
XwinNMR3.5Brukerprocessing
ccnmr/glxccn.a.Cieslar, Holak, Oschkinat, 1990data analysis
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, explicit inclusion of water molecules (Linge, Nilges, 1999)
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
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