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- PDB-1fhd: CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMID... -

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Basic information

Entry
Database: PDB / ID: 1fhd
TitleCRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR
ComponentsBETA-1,4-XYLANASEXylanase
KeywordsHYDROLASE / xylanase / glycosyl hydrolase family 10 / catalytic mechanism / inhibitor
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-XIM / beta-D-xylopyranose / : / Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsNotenboom, V. / Williams, S.J. / Hoos, R. / Withers, S.G. / Rose, D.R.
CitationJournal: Biochemistry / Year: 2000
Title: Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
Authors: Notenboom, V. / Williams, S.J. / Hoos, R. / Withers, S.G. / Rose, D.R.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: 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 / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-1,4-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3723
Polymers34,0521
Non-polymers3202
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.343, 85.343, 78.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1006-

HOH

21A-1056-

HOH

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Components

#1: Protein BETA-1,4-XYLANASE / Xylanase / CEX


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) / Production host: Escherichia coli (E. coli)
References: GenBank: 144429, UniProt: P07986*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-XIM / 5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / XYLOSE-DERIVED IMIDAZOLE


Mass: 170.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H10N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG4K, 0.1M NaAcetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Bedarkar, S., (1992) J.Mol. Biol, 228, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
165 mg/mlCex1drop
27.5-10 %PEG40001drop
30.1 Msodium acetate1drop
47.5-10 %PEG40001reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 415786 / Num. obs: 24224 / % possible obs: 97.2 % / Observed criterion σ(F): 28 / Observed criterion σ(I): 14 / Redundancy: 20 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.256 / % possible all: 83.8
Reflection shell
*PLUS
% possible obs: 83.8 % / Mean I/σ(I) obs: 5.5

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 402753.72 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2239 9.9 %RANDOM
Rwork0.193 ---
obs0.193 22695 97 %-
all-415786 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.89 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 21 250 2671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 339 9.8 %
Rwork0.221 3134 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4CIS-THR81.PEP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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