[English] 日本語
Yorodumi
- PDB-1cx1: SECOND N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FIMI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cx1
TitleSECOND N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FIMI BETA-1,4-GLUCANASE C, NMR, 22 STRUCTURES
ComponentsENDOGLUCANASE C
KeywordsHYDROLASE / CELLULOSE-BINDING DOMAIN / CELLOOLIGOSACHARIDES / CELLULASE / PROTEIN- CARBOHYDRATE INTERACTION
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Carbohydrate-binding, CenC-like ...Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding domain-like / Immunoglobulin I-set / Immunoglobulin I-set domain / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCellulomonas fimi (bacteria)
MethodSOLUTION NMR / ALL CALCULATIONS WERE PERFORMED USING X-PLOR V3.8 WITH SCRIPTS FROM THE X-PLOR 3.1 MANUAL A. A. BRUNGER (1992), NEW HAVEN: YALE UNIVERSITY PRESS ACCORDING TO THE METHOD DESCRIBED BY M. NILGES, G. M. CLORE, A. M. GRONENBORN
Model type detailsminimized average
AuthorsBrun, E. / Johnson, P.E. / Creagh, L.A. / Haynes, C.A. / Tomme, P. / Webster, P. / Kilburn, D.G. / McIntosh, L.P.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C.
Authors: Brun, E. / Johnson, P.E. / Creagh, A.L. / Tomme, P. / Webster, P. / Haynes, C.A. / McIntosh, L.P.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The cellulose-binding domains from Cellulomonas fimi beta-1, 4-glucanase CenC bind nitroxide spin-labeled cellooligosaccharides in multiple orientations
Authors: Brun, E. / Johnson, P.E. / MacKenzie, L. / Withers, S.G. / McIntosh, L.P.
#2: Journal: Biochemistry / Year: 1997
Title: Structure of the N-terminal Cellulose-Binding Domain of Cellulomonas Fimi CenC Determined by Nucelar Magnetic Resonance Spectroscopy
Authors: Johnson, P.E. / Joshi, M.D. / Tomme, P. / Kilburn, D.G. / McIntosh, L.P.
History
DepositionAug 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOGLUCANASE C


Theoretical massNumber of molelcules
Total (without water)15,8771
Polymers15,8771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 60STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #22minimized average structure

-
Components

#1: Protein ENDOGLUCANASE C


Mass: 15877.379 Da / Num. of mol.: 1 / Fragment: RESIDUES 176-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14090, cellulase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1223D 15N-SEPARATED NOESY
1332D NOESY
1414D 13C/15N-SEPARATED NOESY
152HNHA
NMR detailsText: CBDN2 WAS STUDIED IN THE PRESENCE OF SATURATING CONCENTRATIONS OF CELLOPENTAOSE. HOWEVER, DUE TO SPECTRAL OVERLAP, THE OLIGOSACCHARIDE WAS NOT INCLUDED IN THE STRUCTURE CALCULATIONS

-
Sample preparation

Details
Solution-IDContents
11.5 TO 2 MM CBDN2 U-15N, 13C; UP TO 22-FOLD MOLAR EXCESS OF CELLOPENTAOSE; IN 50 MM NACL, 50 MM PHOSPHATE BUFFER K AT PH* 6.5,
21.5 TO 2 MM CBDN2 U-15N; UP TO 22-FOLD MOLAR EXCESS OF CELLOPENTAOSE; IN 50 MM NACL, 50 MM PHOSPHATE BUFFER K AT PH* 6.5,
31.5 TO 2 MM CBDN2 UNLABELED; UP TO 22-FOLD MOLAR EXCESS OF CELLOPENTAOSE; IN 50 MM NACL, 50 MM PHOSPHATE BUFFER K AT PH* 6.5,
Sample conditionsIonic strength: 50mMNACL / pH: 6 / Pressure: 1 atm / Temperature: 35 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Acollection
FELIX230processing
FELIX230data analysis
X-PLOR3.8structure solution
X-PLOR3.8BRUNGER, A. ET AL.refinement
RefinementMethod: ALL CALCULATIONS WERE PERFORMED USING X-PLOR V3.8 WITH SCRIPTS FROM THE X-PLOR 3.1 MANUAL A. A. BRUNGER (1992), NEW HAVEN: YALE UNIVERSITY PRESS ACCORDING TO THE METHOD DESCRIBED BY M. ...Method: ALL CALCULATIONS WERE PERFORMED USING X-PLOR V3.8 WITH SCRIPTS FROM THE X-PLOR 3.1 MANUAL A. A. BRUNGER (1992), NEW HAVEN: YALE UNIVERSITY PRESS ACCORDING TO THE METHOD DESCRIBED BY M. NILGES, G. M. CLORE, A. M. GRONENBORN
Software ordinal: 1
Details: A TOTAL OF 1510 NOE DERIVED DISTANCE RESTRAINTS THAT COMPRISE 700 INTRARESIDUE, 332 SEQUENTIAL, 83 SHORT RANGE (1<|I-J|<=4), 394 LONG RANGE (|I-J|>4) WERE INCLUDED.. 1 DISULPHIDE BOND DISTANCE RESTRAINT, 86 HYDROGEN BOND RESTRAINTS, 53 PHI ANGLE RESTRAINTS, 70 PSI ANGLE RESTRAINTS, AND 48 CHI1 RESTRAINTS WERE ALSO INCLUDED.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 60 / Conformers submitted total number: 22

+
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