[English] 日本語
Yorodumi
- PDB-5x36: Solution structure of the Family 1 carbohydrate-binding module wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x36
TitleSolution structure of the Family 1 carbohydrate-binding module with mannosylated Ser3
ComponentsExoglucanase 1Cellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / Carbohydrate binding
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Exoglucanase 1
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsFeng, Y. / Tan, Z.
Funding support United States, China, 4items
OrganizationGrant numberCountry
the NSF CAREER AwardCHE-1454925 United States
the National Natural Science Foundation of China31270784 China
the National Natural Science Foundation of China31670735 China
Chinese Government Scholarship201604910035 China
CitationJournal: Biochemistry / Year: 2017
Title: Structural Insight into the Stabilizing Effect of O-Glycosylation
Authors: Chaffey, P.K. / Guan, X. / Chen, C. / Ruan, Y. / Wang, X. / Tran, A.H. / Koelsch, T.N. / Cui, Q. / Feng, Y. / Tan, Z.
History
DepositionFeb 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9262
Polymers3,7461
Non-polymers1801
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area190 Å2
ΔGint2 kcal/mol
Surface area2470 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Exoglucanase 1 / Cellulose 1,4-beta-cellobiosidase / 1 / 4-beta-cellobiohydrolase / Exocellobiohydrolase I / CBHI / Exoglucanase I


Mass: 3746.126 Da / Num. of mol.: 1 / Fragment: UNP residues 478-513 / Source method: obtained synthetically / Source: (synth.) Hypocrea jecorina (fungus)
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D DQF-COSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-13C HSQC-TOCSY
161isotropic12D 1H-15N HSQC
172isotropic12D 1H-1H TOCSY
182isotropic12D DQF-COSY
192isotropic12D 1H-1H NOESY
1102isotropic12D 1H-13C HSQC
1112isotropic12D 1H-13C HSQC-TOCSY
1122isotropic12D 1H-13C H2BC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution15 mg/mL CBM, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2Ocbm-h2o90% H2O/10% D2O
solution25 mg/mL CBM, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2Ocbm-d2o100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mg/mLCBMnatural abundance1
50 mMsodium acetate[U-2H]1
0.1 mg/mLDSSnatural abundance1
5 mg/mLCBMnatural abundance2
50 mMsodium acetate[U-2H]2
0.1 mg/mLDSSnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
SANEDuggan, Legge, Dyson & Wrightstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 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