[English] 日本語
Yorodumi
- PDB-2bgp: Mannan Binding Module from Man5C in bound conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bgp
TitleMannan Binding Module from Man5C in bound conformation
ComponentsENDO-B1,4-MANNANASE 5C
KeywordsCARBOHYDRATE BINDING PROTEIN / MANNAN / CARBOHYDRATE BINDING MODULE
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase activity / cellulose binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Mannan endo-1,4-beta-mannosidase-like / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate binding module (family 35) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 ...Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Mannan endo-1,4-beta-mannosidase-like / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate binding module (family 35) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Carbohydrate binding module family 6 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-b1,4-mannanase 5C
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodSOLUTION NMR
AuthorsTunnicliffe, R.B. / Bolam, D.N. / Pell, G. / Gilbert, H.J. / Williamson, M.P.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of a Mannan-Specific Family 35 Carbohydrate-Binding Module: Evidence for Significant Conformational Changes Upon Ligand Binding
Authors: Tunnicliffe, R.B. / Bolam, D.N. / Pell, G. / Gilbert, H.J. / Williamson, M.P.
History
DepositionJan 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDO-B1,4-MANNANASE 5C


Theoretical massNumber of molelcules
Total (without water)14,9481
Polymers14,9481
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)5 / 80RANDOM 5 STRUCTURES FROM 20 LOWEST ENERGY
RepresentativeModel #1

-
Components

#1: Protein ENDO-B1,4-MANNANASE 5C / CBM35 FROM BETA-1 / 4-MANNANASE MAN5C


Mass: 14947.636 Da / Num. of mol.: 1 / Fragment: RESIDUES 197-328
Source method: isolated from a genetically manipulated source
Details: MANNAN SPECIFIC CARBOHYDRATE BINDING MODULE / Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Plasmid: PGP1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 (DE3) / References: UniProt: Q840C0
Sequence detailsPROTEIN SEQUENCE STARTS AT RESIDUE 204 OF FULL LENGTH PROTEIN. ACTUAL PROTEIN SAMPLE CONTAINED ...PROTEIN SEQUENCE STARTS AT RESIDUE 204 OF FULL LENGTH PROTEIN. ACTUAL PROTEIN SAMPLE CONTAINED RESIDUES 197-328 PLUS HIS-TAG SEQUENCE LEHHHHHH AT C-TERMINUS.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE EXPERIMENTS
121HNHA
13115N
14113C-EDITED NOESY
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 50MM SODIUM PHOSPHATE, 10% D2O
Sample conditionspH: 6 / Temperature: 298.0 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Felixstructure solution
CNSstructure solution
NMR ensembleConformer selection criteria: RANDOM 5 STRUCTURES FROM 20 LOWEST ENERGY
Conformers calculated total number: 80 / Conformers submitted total number: 5

+
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