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- PDB-5zqx: Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5zqx
TitleCrystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus
ComponentsBeta-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 ...: / 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-xylosidase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_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_atom_id / _atom_site.label_comp_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
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
C: Beta-xylosidase
D: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,4878
Polymers248,3584
Non-polymers1,1294
Water18,6091033
1
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7434
Polymers124,1792
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-23 kcal/mol
Surface area37570 Å2
MethodPISA
2
C: Beta-xylosidase
D: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7434
Polymers124,1792
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-25 kcal/mol
Surface area37540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.259, 104.776, 113.163
Angle α, β, γ (deg.)90.00, 111.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 62089.488 Da / Num. of mol.: 4 / Mutation: E186Q
Source method: isolated from a genetically manipulated source
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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1033 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M HEPES (pH 7.5), 20%(w/v) PEG 3350, 1%(w/v) tryptone, and 30mM xylobiose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 143588 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.079 / Χ2: 18.7 / Net I/σ(I): 16.64
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.84 / Num. unique obs: 6694 / CC1/2: 0.644 / Rpim(I) all: 0.211 / Rrim(I) all: 0.399 / Χ2: 22.8 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQJ

5zqj


Resolution: 2→30.7 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.2142 6799 5 %
Rwork0.1698 --
obs0.1721 136082 89.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17318 0 76 1033 18427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417943
X-RAY DIFFRACTIONf_angle_d0.71324415
X-RAY DIFFRACTIONf_dihedral_angle_d4.00910409
X-RAY DIFFRACTIONf_chiral_restr0.0492559
X-RAY DIFFRACTIONf_plane_restr0.0053144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02180.26671220.22142543X-RAY DIFFRACTION52
2.0218-2.04560.30611510.22942897X-RAY DIFFRACTION61
2.0456-2.07050.29261860.21993250X-RAY DIFFRACTION68
2.0705-2.09670.27421890.22273488X-RAY DIFFRACTION73
2.0967-2.12430.26532000.21783684X-RAY DIFFRACTION77
2.1243-2.15340.29211860.21293924X-RAY DIFFRACTION81
2.1534-2.18410.27422310.20854056X-RAY DIFFRACTION85
2.1841-2.21670.27182180.20294100X-RAY DIFFRACTION87
2.2167-2.25130.25272350.20164277X-RAY DIFFRACTION89
2.2513-2.28820.24922150.1934286X-RAY DIFFRACTION89
2.2882-2.32770.2292060.1954343X-RAY DIFFRACTION91
2.3277-2.370.24982230.20234444X-RAY DIFFRACTION92
2.37-2.41560.25242010.20074477X-RAY DIFFRACTION92
2.4156-2.46490.26552380.19714401X-RAY DIFFRACTION92
2.4649-2.51840.24542280.18854498X-RAY DIFFRACTION93
2.5184-2.5770.24082320.18814482X-RAY DIFFRACTION94
2.577-2.64140.25192510.18894552X-RAY DIFFRACTION95
2.6414-2.71280.25622360.18484620X-RAY DIFFRACTION96
2.7128-2.79250.23242300.18954644X-RAY DIFFRACTION96
2.7925-2.88260.26112330.18734658X-RAY DIFFRACTION97
2.8826-2.98560.23082370.18044667X-RAY DIFFRACTION97
2.9856-3.1050.23072460.17714701X-RAY DIFFRACTION98
3.105-3.24620.23322520.17284728X-RAY DIFFRACTION98
3.2462-3.41710.19832510.16334787X-RAY DIFFRACTION99
3.4171-3.63090.17952620.1444743X-RAY DIFFRACTION99
3.6309-3.91070.18262460.13914790X-RAY DIFFRACTION99
3.9107-4.30330.15752660.13064815X-RAY DIFFRACTION100
4.3033-4.92380.16152640.1294818X-RAY DIFFRACTION100
4.9238-6.19510.1872900.14464791X-RAY DIFFRACTION100
6.1951-30.70.16462740.15394819X-RAY DIFFRACTION98

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