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- PDB-9j08: Acetyl xylan esterase B from Aspergillus oryzae (AoAXEB), succina... -

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Basic information

Entry
Database: PDB / ID: 9j08
TitleAcetyl xylan esterase B from Aspergillus oryzae (AoAXEB), succinate complex form
Componentsferuloyl esterase
KeywordsHYDROLASE / Acetyl xylan esterase
Function / homology
Function and homology information


feruloyl esterase / feruloyl esterase activity / xylan catabolic process / extracellular region
Similarity search - Function
Feruloyl esterase B/C/D / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / SUCCINIC ACID / feruloyl esterase
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYamada, C. / Koseki, T. / Fushinobu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2025
Title: Identification and structural characterization of a novel acetyl xylan esterase from Aspergillus oryzae.
Authors: Yamada, C. / Kato, T. / Shiono, Y. / Koseki, T. / Fushinobu, S.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2105
Polymers35,5901
Non-polymers6204
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint6 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.027, 64.008, 83.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein feruloyl esterase


Mass: 35590.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: AO090005000945 / Plasmid: pPICZB / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q2UR69, feruloyl esterase
#2: 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.: 2 / Source method: isolated from a natural 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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate (pH 4.5), 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.1 Å / Num. obs: 23666 / % possible obs: 96 % / Redundancy: 5.6 % / Biso Wilson estimate: 11.56 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1011 / CC1/2: 0.715 / Rpim(I) all: 0.176 / % possible all: 65.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.1 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.731 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19942 1179 5 %RANDOM
Rwork0.16367 ---
obs0.16545 22442 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å20 Å2
2---0.94 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.9→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 40 245 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162133
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6783301
X-RAY DIFFRACTIONr_angle_other_deg0.5131.5814944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5315298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.494513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23410345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7331.5021193
X-RAY DIFFRACTIONr_mcbond_other1.7321.51192
X-RAY DIFFRACTIONr_mcangle_it2.6912.6751487
X-RAY DIFFRACTIONr_mcangle_other2.692.681488
X-RAY DIFFRACTIONr_scbond_it2.5041.7691229
X-RAY DIFFRACTIONr_scbond_other2.51.7691228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.013.1251814
X-RAY DIFFRACTIONr_long_range_B_refined6.06116.222778
X-RAY DIFFRACTIONr_long_range_B_other5.95815.552704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 66 -
Rwork0.193 1126 -
obs--66.93 %

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