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- PDB-8iyc: Structure insight into substrate recognition and catalysis by fer... -

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Basic information

Entry
Database: PDB / ID: 8iyc
TitleStructure insight into substrate recognition and catalysis by feruloyl esterase from Aspergillus sydowii
ComponentsFeruloyl esterase
KeywordsHYDROLASE / Feruloyl esterase / complex / sinapic acid
Function / homology
Function and homology information


acetylxylan esterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / xylan catabolic process / extracellular region
Similarity search - Function
Esterase, PHB depolymerase / Esterase PHB depolymerase / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / SINAPINATE / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesAspergillus sydowii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPhienluphon, A. / Kondo, K. / Mikami, B. / Nagata, T. / Katahira, M.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03192 Japan
Japan Society for the Promotion of Science (JSPS)20K21477 Japan
Japan Society for the Promotion of Science (JSPS)21H05519 Japan
Japan Society for the Promotion of Science (JSPS)22H05596 Japan
Japan Society for the Promotion of Science (JSPS)20K06524 Japan
Japan Society for the Promotion of Science (JSPS)20K06164 Japan
Citation
Journal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii.
Authors: Phienluphon, A. / Kondo, K. / Mikami, B. / Nagata, T. / Katahira, M.
#1: Journal: Bull Soc Ophtalmol Fr / Year: 1987
Title: [Treatment of vitreous hemorrhages. Rare causes].
Authors: Aracil, P.
History
DepositionApr 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: Feruloyl esterase
B: Feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,24729
Polymers60,6342
Non-polymers2,61227
Water6,810378
1
A: Feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,59514
Polymers30,3171
Non-polymers1,27813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,65115
Polymers30,3171
Non-polymers1,33414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.378, 65.258, 95.381
Angle α, β, γ (deg.)90.000, 96.995, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Feruloyl esterase / Carboxylic ester hydrolase


Mass: 30317.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus sydowii (mold) / Gene: ASPSYDRAFT_1158585 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: A0A1L9T9J3
#3: 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 4 types, 401 molecules

#2: Chemical ChemComp-SXX / SINAPINATE


Mass: 224.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Ammonium acetate, 0.1 M sodium acetate, 30%(w/v) PEG 4000, 10 mM sinapic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 65419 / % possible obs: 98.2 % / Redundancy: 4.51 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.033 / Net I/σ(I): 26.05
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.61 / Num. unique obs: 10051 / CC1/2: 0.955 / Rrim(I) all: 0.272 / % possible all: 93.5

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Processing

Software
NameVersionClassification
BSSdata collection
XDSJan10, 2022data reduction
XDSJan10, 2022data scaling
MOLREP11.7.01phasing
PHENIX1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IY8

8iy8


Resolution: 1.55→32.63 Å / SU ML: 0.1659 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.2149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1857 3272 5 %
Rwork0.1339 62132 -
obs0.1365 65404 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.73 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 172 378 4708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00564525
X-RAY DIFFRACTIONf_angle_d0.80116171
X-RAY DIFFRACTIONf_chiral_restr0.0556661
X-RAY DIFFRACTIONf_plane_restr0.0059820
X-RAY DIFFRACTIONf_dihedral_angle_d8.7741661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.28851230.22182325X-RAY DIFFRACTION84.76
1.57-1.590.26551370.18442608X-RAY DIFFRACTION95.74
1.59-1.620.22981410.17282670X-RAY DIFFRACTION97.1
1.62-1.650.21061390.15522655X-RAY DIFFRACTION97.73
1.65-1.680.2111430.14282717X-RAY DIFFRACTION98.35
1.68-1.710.21511430.14142710X-RAY DIFFRACTION98.41
1.71-1.740.20641400.1442656X-RAY DIFFRACTION98.69
1.74-1.780.23671450.13652746X-RAY DIFFRACTION98.74
1.78-1.820.20861390.12662655X-RAY DIFFRACTION99.01
1.82-1.870.20231470.11872784X-RAY DIFFRACTION98.95
1.87-1.920.16791420.12822688X-RAY DIFFRACTION99.09
1.92-1.980.2041430.13172734X-RAY DIFFRACTION99
1.98-2.040.21621430.13352701X-RAY DIFFRACTION99.13
2.04-2.110.20431430.12372717X-RAY DIFFRACTION99.27
2.11-2.20.18281440.12262730X-RAY DIFFRACTION99.04
2.2-2.30.19381420.12522710X-RAY DIFFRACTION99.27
2.3-2.420.16631450.12282755X-RAY DIFFRACTION99.49
2.42-2.570.16341440.12892729X-RAY DIFFRACTION99.45
2.57-2.770.19171440.13272732X-RAY DIFFRACTION99.17
2.77-3.050.17961440.13842741X-RAY DIFFRACTION99.11
3.05-3.490.16181460.13122769X-RAY DIFFRACTION99.73
3.49-4.390.17031450.12182769X-RAY DIFFRACTION99.56
4.39-32.630.18261500.14762831X-RAY DIFFRACTION99.43

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