[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleA structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis.
Journal, issue, pagesJ. Biol. Chem., Vol. 295, Page 17752-17769, Year 2020
Publish dateJan 2, 2013 (structure data deposition date)
AuthorsGlasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G.
External linksJ. Biol. Chem. / PubMed:33454012
MethodsX-ray diffraction
Resolution1.05 - 2.42 Å
Structure data

PDB-4im4:
Multifunctional cellulase, xylanase, mannanase
Method: X-RAY DIFFRACTION / Resolution: 2.42 Å

PDB-6mq4:
GH5-4 broad specificity endoglucanase from Hungateiclostridium cellulolyticum
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-6pz7:
GH5-4 broad specificity endoglucanase from Clostridium acetobutylicum
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-6q1i:
GH5-4 broad specificity endoglucanase from Clostrdium longisporum
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-6ui3:
GH5-4 broad specificity endoglucanase from Clostridum cellulovorans
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-6wqp:
GH5-4 broad specificity endoglucanase from Ruminococcus champanellensis
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-6wqv:
GH5-4 broad specificity endoglucanase from Ruminococcus champanellensis with bound cellotriose
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6wqy:
GH5-4 broad specificity endoglucanase from Bacteroides salanitronis
Method: X-RAY DIFFRACTION / Resolution: 1.05 Å

PDB-6xrk:
GH5-4 broad specificity endoglucanase from an uncultured bovine rumen ciliate
Method: X-RAY DIFFRACTION / Resolution: 1.419 Å

PDB-6xso:
GH5-4 broad specificity endoglucanase from an uncultured bacterium
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6xsu:
GH5-4 broad specificity endoglucanase from Ruminococcus flavefaciens
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-CL:
Unknown entry / Chloride

ChemComp-NA:
Unknown entry

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

ChemComp-NO3:
NITRATE ION / Nitrate

ChemComp-MG:
Unknown entry

ChemComp-BTB:
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Bis-tris methane

ChemComp-LMR:
(2S)-2-hydroxybutanedioic acid / Malic acid

ChemComp-EOH:
ETHANOL / Ethanol

Source
  • clostridium thermocellum (bacteria)
  • hungateiclostridium cellulolyticum (bacteria)
  • clostridium acetobutylicum atcc 824 (bacteria)
  • clostridium longisporum (bacteria)
  • clostridium cellulovorans (bacteria)
  • ruminococcus champanellensis (bacteria)
  • bacteroides salanitronis (strain dsm 18170 / jcm 13567 / bl78) (bacteria)
  • uncultured bovine rumen ciliate (environmental samples)
  • uncultured bacterium (environmental samples)
  • ruminococcus flavefaciens (bacteria)
KeywordsHYDROLASE / cellulase / xylanase / mannanase / multifunction / Endo-1 / 4-beta-glucanase / biomass degradation / manganese / GH5 / endoglucanase / GH5-4 / GLBRC

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more