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- PDB-7yo6: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -

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Basic information

Entry
Database: PDB / ID: 7yo6
TitleBifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose for 1.5min
ComponentsBeta-D-xylosidase/beta-D-glucosidase
KeywordsHYDROLASE / glycoside hydrolases / xylosidases / bifunctional
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region
Similarity search - Function
: / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily ...: / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Deacetyltaxol / Xylitol / beta-D-xylofuranose / Probable beta-glucosidase G
Similarity search - Component
Biological speciesLentinula edodes (shiitake mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsYang, L.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270796 China
CitationJournal: To Be Published
Title: Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose
Authors: Yang, L.Y.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-D-xylosidase/beta-D-glucosidase
B: Beta-D-xylosidase/beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,00520
Polymers172,0742
Non-polymers6,93218
Water13,169731
1
A: Beta-D-xylosidase/beta-D-glucosidase
hetero molecules

A: Beta-D-xylosidase/beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,08022
Polymers172,0742
Non-polymers7,00720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9620 Å2
ΔGint63 kcal/mol
Surface area47520 Å2
MethodPISA
2
B: Beta-D-xylosidase/beta-D-glucosidase
hetero molecules

B: Beta-D-xylosidase/beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,93018
Polymers172,0742
Non-polymers6,85716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10190 Å2
ΔGint64 kcal/mol
Surface area47560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.594, 181.920, 241.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-D-xylosidase/beta-D-glucosidase


Mass: 86036.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinula edodes (shiitake mushroom) / Gene: Lxyl-p1-2 / Production host: Escherichia coli (E. coli) / References: UniProt: G8GLP2

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Sugars , 6 types, 16 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-1)-alpha-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-1)-alpha-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 789.734 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-1DManpa3-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
[][D-1-deoxy-Manp]{[(3+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-XYZ / beta-D-xylofuranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylofuranoseCOMMON NAMEGMML 1.0
b-D-XylfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O5 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 2 types, 733 molecules

#6: Chemical ChemComp-BKR / Deacetyltaxol


Mass: 811.869 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H49NO13
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 15% PEG3350, pH 8.0 Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.539→200 Å / Num. obs: 57972 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.976 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.6
Reflection shellResolution: 2.539→2.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2855 / CC1/2: 0.937 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EY1

7ey1


Resolution: 2.54→120.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.74 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.815 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2812 4.9 %RANDOM
Rwork0.1905 ---
obs0.1941 55135 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.67 Å2 / Biso mean: 33.39 Å2 / Biso min: 11.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å20 Å2-0 Å2
2---1.69 Å20 Å2
3----1.72 Å2
Refinement stepCycle: final / Resolution: 2.54→120.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11419 0 467 731 12617
Biso mean--47.87 30.6 -
Num. residues----1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212215
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211109
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9916740
X-RAY DIFFRACTIONr_angle_other_deg1.082325605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11951511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3324.699498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.978151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2511550
X-RAY DIFFRACTIONr_chiral_restr0.0980.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022700
LS refinement shellResolution: 2.54→2.605 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.351 199 -
Rwork0.27 3789 -
obs--93.53 %

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