[English] 日本語
Yorodumi
- PDB-2mpk: Characterization and structure of the MIT1 domain of a chitin syn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mpk
TitleCharacterization and structure of the MIT1 domain of a chitin synthase from the Oomycete Saprolegnia monoica
ComponentsChitin synthase 1
KeywordsTRANSFERASE / MIT domain / three-helix bundle / Saprolegnia / Oomycete / carbohydrate synthase / microtubule interacting and trafficking domain
Function / homology
Function and homology information


chitin biosynthetic process / chitin synthase / chitin synthase activity / membrane
Similarity search - Function
Chitin synthase N-terminal / Chitin synthase N-terminal / Fungal chitin synthase / Chitin synthase / Chitin synthase / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / Nucleotide-diphospho-sugar transferases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaprolegnia monoica (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBulone, V. / Szpryngiel, S. / Brown, C. / Ye, W.
CitationJournal: Febs J. / Year: 2016
Title: Structural and functional characterization of the microtubule interacting and trafficking domains of two oomycete chitin synthases.
Authors: Brown, C. / Szpryngiel, S. / Kuang, G. / Srivastava, V. / Ye, W. / McKee, L.S. / Tu, Y. / Maler, L. / Bulone, V.
History
DepositionMay 27, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chitin synthase 1


Theoretical massNumber of molelcules
Total (without water)8,5281
Polymers8,5281
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Chitin synthase 1


Mass: 8527.657 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 103-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saprolegnia monoica (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D7NQS8, chitin synthase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY

-
Sample preparation

DetailsContents: 0.3-1.0 mM [U-100% 13C; U-100% 15N] SmChs_MIT1-1, 10 % D2O-2, 50 mM sodium phosphate-3, 150 mM sodium chloride-4, 90 % H2O-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSmChs_MIT1-1[U-100% 13C; U-100% 15N]0.3-1.01
10 %D2O-21
50 mMsodium phosphate-31
150 mMsodium chloride-41
90 %H2O-51
Sample conditionsIonic strength: 200 / pH: 5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE5003

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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