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- PDB-5zqs: Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Ba... -

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Basic information

Entry
Database: PDB / ID: 5zqs
TitleCrystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus
ComponentsBeta-xylosidaseXylan 1,4-b-xylosidase
KeywordsHYDROLASE / xylobiose hydrolysis
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4beta-beta-xylobiose / beta-D-xylopyranose / Beta-xylosidase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsHa, N.C. / Hong, S. / Jo, I.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose
Authors: Hong, S. / Kyung, M. / Jo, I. / Kim, Y.R. / Ha, N.C.
History
DepositionApr 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9265
Polymers124,2112
Non-polymers7153
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-25 kcal/mol
Surface area36930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.021, 103.437, 104.813
Angle α, β, γ (deg.)90.00, 123.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 62105.488 Da / Num. of mol.: 2 / Mutation: E186Q, F503Y
Source method: isolated from a genetically manipulated source
Details: Electron map was not observed between 272-274. / Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: xynB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07129, xylan 1,4-beta-xylosidase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: 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.: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 42.51 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M HEPES (pH 7.5), 20% (w/v) PEG 3350, 1% (w/v) tryptone, and 30 mM xylobiose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 95015 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Χ2: 0.87 / Net I/σ(I): 13.86
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 4377 / CC1/2: 0.268 / Rpim(I) all: 0.298 / Rrim(I) all: 0.558 / Χ2: 0.763 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQJ

5zqj


Resolution: 1.782→35.633 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 20.33
RfactorNum. reflection% reflection
Rfree0.2093 4243 5.09 %
Rwork0.1658 --
obs0.168 83428 83.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.782→35.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 48 555 9219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078937
X-RAY DIFFRACTIONf_angle_d0.91612162
X-RAY DIFFRACTIONf_dihedral_angle_d4.1165177
X-RAY DIFFRACTIONf_chiral_restr0.0591277
X-RAY DIFFRACTIONf_plane_restr0.0071563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7824-1.80270.2464510.16731156X-RAY DIFFRACTION37
1.8027-1.82390.2088940.1811387X-RAY DIFFRACTION45
1.8239-1.84620.2314780.18021537X-RAY DIFFRACTION49
1.8462-1.86950.2325930.18291585X-RAY DIFFRACTION51
1.8695-1.89410.2326860.181791X-RAY DIFFRACTION57
1.8941-1.92010.20871110.18451887X-RAY DIFFRACTION60
1.9201-1.94750.29441190.19022054X-RAY DIFFRACTION66
1.9475-1.97660.20281120.18192164X-RAY DIFFRACTION70
1.9766-2.00740.23051090.18642341X-RAY DIFFRACTION73
2.0074-2.04040.2581460.18642477X-RAY DIFFRACTION80
2.0404-2.07550.22541420.17642648X-RAY DIFFRACTION85
2.0755-2.11330.23491550.17982782X-RAY DIFFRACTION88
2.1133-2.15390.26241290.17392885X-RAY DIFFRACTION92
2.1539-2.19790.19651400.17322956X-RAY DIFFRACTION93
2.1979-2.24560.2181480.18072964X-RAY DIFFRACTION95
2.2456-2.29790.24691520.17573042X-RAY DIFFRACTION95
2.2979-2.35530.21441680.1792990X-RAY DIFFRACTION96
2.3553-2.4190.23241570.17863044X-RAY DIFFRACTION97
2.419-2.49020.22751660.17183074X-RAY DIFFRACTION97
2.4902-2.57050.24591790.183051X-RAY DIFFRACTION98
2.5705-2.66240.21411700.18223111X-RAY DIFFRACTION98
2.6624-2.76890.21061650.17973098X-RAY DIFFRACTION98
2.7689-2.89490.23521710.18143125X-RAY DIFFRACTION99
2.8949-3.04740.21141870.16723071X-RAY DIFFRACTION99
3.0474-3.23820.21571670.17063160X-RAY DIFFRACTION99
3.2382-3.48810.20212030.16513089X-RAY DIFFRACTION99
3.4881-3.83870.20571690.14813154X-RAY DIFFRACTION100
3.8387-4.39330.17331690.13683163X-RAY DIFFRACTION100
4.3933-5.53180.15591530.13693189X-RAY DIFFRACTION99
5.5318-35.64040.18621540.15853210X-RAY DIFFRACTION99

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