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- PDB-1j01: Crystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhi... -

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Basic information

Entry
Database: PDB / ID: 1j01
TitleCrystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhibitor Isofagomine lactam
Componentsbeta-1,4-xylanase
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 / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / polysaccharide binding / 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. / Glycosyl hydrolases family 10 (GH10) domain profile. ...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. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

#1: Protein beta-1,4-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


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

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Experimental details

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Experiment

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

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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

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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

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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

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