[English] 日本語
Yorodumi
- PDB-2rv9: Solution structure of chitosan-binding module 1 derived from chit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rv9
TitleSolution structure of chitosan-binding module 1 derived from chitosanase/glucanase from Paenibacillus sp. IK-5
ComponentsGlucanase
KeywordsHYDROLASE / carbohydrate-binding module / CBM / chitosanase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / NedA-like, galactose-binding domain / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Six-hairpin glycosidase-like superfamily ...Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / NedA-like, galactose-binding domain / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding domain-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus fukuinensis (bacteria)
MethodSOLUTION NMR / na
Model detailslowest energy, model1
AuthorsShinya, S. / Nishimura, S. / Fukamizo, T.
CitationJournal: Biochem.J. / Year: 2016
Title: Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase.
Authors: Shinya, S. / Nishimura, S. / Kitaoku, Y. / Numata, T. / Kimoto, H. / Kusaoke, H. / Ohnuma, T. / Fukamizo, T.
History
DepositionMay 12, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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: Glucanase


Theoretical massNumber of molelcules
Total (without water)14,9221
Polymers14,9221
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)10 / 3000target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Glucanase / chitosanase


Mass: 14922.099 Da / Num. of mol.: 1 / Fragment: chitosan-binding module 1, UNP residues 530-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus fukuinensis (bacteria) / Strain: IK-5
Description: Paenibacillus fukuinensis has been renamed to Paenibacillus sp. IK-5.
Production host: Escherichia coli (E. coli)
References: UniProt: Q93IE7, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1822D 1H-13C HSQC
1923D (H)CCH-TOCSY
11023D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
110 mM TRIS-1, 0.4 mM [U-95% 13C; U-95% 15N] DD1-2, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-95% 13C; U-95% 15N] DD1-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMTRIS-11
0.4 mMDD1-2[U-95% 13C; U-95% 15N]1
0.4 mMDD1-3[U-95% 13C; U-95% 15N]2
Sample conditionspH: 7 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
TALOSCornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: na / Software ordinal: 1
NMR constraintsNOE constraints total: 893 / Hydrogen bond constraints total count: 44 / Protein chi angle constraints total count: 146 / Protein other angle constraints total count: 77 / Protein phi angle constraints total count: 135 / Protein psi angle constraints total count: 120
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 3000 / Conformers submitted total number: 10 / 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