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- PDB-1px8: Crystal structure of beta-D-xylosidase from Thermoanaerobacterium... -

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Basic information

Entry
Database: PDB / ID: 1px8
TitleCrystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase
ComponentsBeta-xylosidaseXylan 1,4-b-xylosidase
KeywordsHYDROLASE / family 39 glycoside hydrolase / xylosidase / xylan / xylose / covalent glycosyl-enzyme intermediate
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-xylopyranose / Beta-xylosidase
Similarity search - Component
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsYang, J.K. / Yoon, H.J. / Ahn, H.J. / Il Lee, B. / Pedelacq, J.D. / Liong, E.C. / Berendzen, J. / Laivenieks, M. / Vieille, C. / Zeikus, G.J. ...Yang, J.K. / Yoon, H.J. / Ahn, H.J. / Il Lee, B. / Pedelacq, J.D. / Liong, E.C. / Berendzen, J. / Laivenieks, M. / Vieille, C. / Zeikus, G.J. / Vocadlo, D.J. / Withers, S.G. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase.
Authors: Yang, J.K. / Yoon, H.J. / Ahn, H.J. / Lee, B.I. / Pedelacq, J.D. / Liong, E.C. / Berendzen, J. / Laivenieks, M. / Vieille, C. / Zeikus, G.J. / Vocadlo, D.J. / Withers, S.G. / Suh, S.W.
History
DepositionJul 3, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7794
Polymers117,4782
Non-polymers3002
Water5,891327
1
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules

A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,5578
Polymers234,9574
Non-polymers6014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area18770 Å2
ΔGint-60 kcal/mol
Surface area69780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.719, 92.719, 241.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Beta-xylosidase / Xylan 1,4-b-xylosidase / 1 / 4-beta-D-xylosidase / 1 / 4-beta-D-xylan xylohydrolase / Xylan 1 / 4-beta-xylosidase


Mass: 58739.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Plasmid: pXHP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P36906, xylan 1,4-beta-xylosidase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.14 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000 MME, Tris-HCl, dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: Yang, J.K., (2002) Acta Crystallogr., D58, 531.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.0 MD-xylose1drop
324 %(w/v)PEG2000MME1reservoir
45 mMdithiothreitol1reservoir
50.1 MTris-HCl1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9500, 0.9787, 0.9789, 1.0000
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 10, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97871
30.97891
411
ReflectionResolution: 2.4→20 Å / Num. all: 37528 / Num. obs: 35679 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12 Å2 / Rsym value: 0.066 / Net I/σ(I): 15.1
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.247 / % possible all: 76.6
Reflection
*PLUS
Num. obs: 37528 / Num. measured all: 172649 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 76.6 % / Rmerge(I) obs: 0.247

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.91 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3580 10 %RANDOM
Rwork0.224 ---
all0.229 37437 --
obs0.224 35677 84.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.7696 Å2 / ksol: 0.28452 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å20 Å20 Å2
2--4.69 Å20 Å2
3----9.39 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.57 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8308 0 20 327 8655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.472.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 476 10.2 %
Rwork0.332 4204 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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