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

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Basic information

Entry
Database: PDB / ID: 1uhv
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
1,5-anhydro-2-deoxy-2-fluoro-D-xylitol / Beta-xylosidase
Similarity search - Component
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Beta-xylosidase
D: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,5018
Polymers234,9574
Non-polymers5444
Water21,9781220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18400 Å2
ΔGint-24 kcal/mol
Surface area69860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.326, 152.276, 159.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the tetramer in a crystallographically asymmetric unit

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Components

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


Mass: 58739.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Plasmid: pXHP3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P36906, xylan 1,4-beta-xylosidase
#2: Sugar
ChemComp-DFX / 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol / 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE


Type: D-saccharide / Mass: 136.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9FO3
IdentifierTypeProgram
D-1-deoxy-Xylp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1220 / 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: 2.32 Å3/Da / Density % sol: 46.49 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9792 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 125254 / Num. obs: 125254 / % possible obs: 92.2 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 6.5 Å2 / Rsym value: 0.074 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.211 / % possible all: 83.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PX8

1px8


Resolution: 2.1→32.33 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 798853.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 12058 10 %RANDOM
Rwork0.21 ---
all0.214 125254 --
obs0.21 120677 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1467 Å2 / ksol: 0.336387 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.2 Å20 Å20 Å2
2---5.18 Å20 Å2
3----9.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.1→32.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16612 0 36 1220 17868
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 1688 9.9 %
Rwork0.332 15278 -
obs--75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.GLX.PAR.V1&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM

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