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- PDB-7vc7: The structure of beta-xylosidase from Phanerochaete chrysosporium... -

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Basic information

Entry
Database: PDB / ID: 7vc7
TitleThe structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)
Componentsxylan 1,4-beta-xylosidase
KeywordsHYDROLASE / Glycoside hydrolase family 3 / beta-xylosidase / HYDROLASE (E.C.3.2.1.37)
Function / homology
Function and homology information


Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / TIM Barrel / Alpha-Beta Barrel / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / beta-D-xylopyranose
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsKojima, K. / Sunagawa, N. / Igarashi, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03013 Japan
Japan Society for the Promotion of Science (JSPS)19K15884 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Comparison of glycoside hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems.
Authors: Kojima, K. / Sunagawa, N. / Mikkelsen, N.E. / Hansson, H. / Karkehabadi, S. / Samejima, M. / Sandgren, M. / Igarashi, K.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 13, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: 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: xylan 1,4-beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,66427
Polymers79,5141
Non-polymers5,15126
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA software showed there are no any specific interactions that could result in the formation of stable quaternary structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint14 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.367, 91.071, 106.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein xylan 1,4-beta-xylosidase


Mass: 79513.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: PcBxl3 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: xylan 1,4-beta-xylosidase

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Sugars , 2 types, 8 molecules

#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.: 7
Source method: isolated from a genetically manipulated source
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
#6: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-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 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 4 types, 186 molecules

#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 525mM Malic acid (pH7.0), 20% v/v PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→44.08 Å / Num. obs: 14756 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 48.53 Å2 / CC1/2: 0.985 / Net I/σ(I): 7.82
Reflection shellResolution: 3.08→3.19 Å / Num. unique obs: 1450 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2-3874)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VC6

7vc6


Resolution: 3.08→44.079 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 720 4.88 %
Rwork0.204 --
obs0.2068 14751 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→44.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 231 168 6116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036092
X-RAY DIFFRACTIONf_angle_d0.7048250
X-RAY DIFFRACTIONf_dihedral_angle_d8.4833603
X-RAY DIFFRACTIONf_chiral_restr0.05926
X-RAY DIFFRACTIONf_plane_restr0.0081046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.31780.33191450.23842747X-RAY DIFFRACTION100
3.3178-3.65150.2871470.21252762X-RAY DIFFRACTION100
3.6515-4.17950.26361220.19092790X-RAY DIFFRACTION100
4.1795-5.26440.23441610.17062793X-RAY DIFFRACTION100
5.2644-44.0790.23781450.22392939X-RAY DIFFRACTION100

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