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- PDB-7yo7: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -

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Basic information

Entry
Database: PDB / ID: 7yo7
TitleBifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 5 seconds
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 / D-xylose / Probable beta-glucosidase G
Similarity search - Component
Biological speciesLentinula edodes (shiitake mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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: Gong, W.M. / Yang, L.Y.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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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)179,00320
Polymers172,0742
Non-polymers6,93018
Water17,529973
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint91 kcal/mol
Surface area50590 Å2
Unit cell
Length a, b, c (Å)80.350, 182.570, 242.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1473-

HOH

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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 phage EcSzw-2 (virus) / References: UniProt: G8GLP2

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Sugars , 5 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: isolated from a genetically manipulated source
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: isolated from a genetically manipulated source
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: isolated from a genetically manipulated source
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-XLS / D-xylose / D-XYLOSE (LINEAR FORM)


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 2 types, 975 molecules

#6: Chemical ChemComp-BKR / Deacetyltaxol


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


Mass: 18.015 Da / Num. of mol.: 973 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 15% PEG3350, 0.1 M Tris-HCl pH8.0, 0.2% MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.81→73.54 Å / Num. obs: 161417 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.056 / Rrim(I) all: 0.148 / Χ2: 0.97 / Net I/σ(I): 10.7
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 14 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11837 / CC1/2: 0.794 / Rpim(I) all: 0.495 / Rrim(I) all: 1.325 / Χ2: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KJ0

6kj0


Resolution: 1.81→73.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.946 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 7850 4.9 %RANDOM
Rwork0.2118 ---
obs0.2137 160806 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.54 Å2 / Biso mean: 35.027 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å2-0 Å2
2---1.12 Å20 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 1.81→73.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11419 0 467 973 12859
Biso mean--45.19 43.88 -
Num. residues----1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212205
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211100
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.98916726
X-RAY DIFFRACTIONr_angle_other_deg1.165325583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09451511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68124.699498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.222151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0351550
X-RAY DIFFRACTIONr_chiral_restr0.1380.21940
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022701
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 551 -
Rwork0.315 11277 -
all-11828 -
obs--99.96 %

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