[English] 日本語
Yorodumi
- PDB-1j01: Crystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j01
TitleCrystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhibitor Isofagomine lactam
Componentsbeta-1,4-xylanaseXylanase
KeywordsHYDROLASE / CEX / XYLANASE / DEOXYNOJIRIMYCIN INHIBITOR / CELLULOSE DEGRADATION
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-XIL / Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWilliams, S.J. / Notenboom, V. / Wicki, J. / Rose, D.R. / Withers, S.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: A New, Simple, High-Affinity Glycosidase Inhibitor: Analysis of Binding through X-ray Crystallography, Mutagenesis, and Kinetic Analysis
Authors: Williams, S.J. / Notenboom, V. / Wicki, J. / Rose, D.R. / Withers, S.G.
History
DepositionOct 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-1,4-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3152
Polymers34,0521
Non-polymers2631
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.996, 86.996, 80.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein beta-1,4-xylanase / Xylanase


Mass: 34051.941 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Gene: Cex / Plasmid: pUC12 / Production host: Escherichia coli (E. coli)
References: UniProt: P07986, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-XIL / (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside / 3-HYDROXY-4-(3,4,5-TRIHYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-PIPERIDIN-2-ONE / (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xyloside / (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl D-xyloside / (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl xyloside


Type: D-saccharide / Mass: 263.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 M11pH4.6NaOAc
216 %PEG400011

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000
RadiationMonochromator: Osmic focussing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 21434 / Num. obs: 20862 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.1 Å / % possible all: 85
Reflection
*PLUS
Num. obs: 21259 / % possible obs: 99 % / Num. measured all: 258208 / Rmerge(I) obs: 0.057

-
Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 2070 random
Rwork0.209 --
all0.21 21434 -
obs0.21 20862 -
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 18 160 2578
Refinement
*PLUS
Lowest resolution: 500 Å / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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