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

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Basic information

Entry
Database: PDB / ID: 8iyb
TitleStructure insight into substrate recognition and catalysis by feruloyl esterase from Aspergillus sydowii
ComponentsFeruloyl esterase
KeywordsHYDROLASE / Feruloyl esterase
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 / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesAspergillus sydowii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)62,57519
Polymers60,6342
Non-polymers1,94117
Water8,971498
1
A: Feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1968
Polymers30,3171
Non-polymers8797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,37911
Polymers30,3171
Non-polymers1,06210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.348, 65.494, 95.293
Angle α, β, γ (deg.)90.000, 96.715, 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) / References: UniProt: A0A1L9T9J3
#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.: 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, 511 molecules

#3: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
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, 10mM ferulic 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: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 71862 / % possible obs: 98.2 % / Redundancy: 4.38 % / Biso Wilson estimate: 15.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.033 / Net I/σ(I): 27.35
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 5.89 / Num. unique obs: 33874 / CC1/2: 0.978 / Rrim(I) all: 0.181 / % possible all: 89.5

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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: 1.5→47.32 Å / SU ML: 0.1318 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.8152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1688 3592 5 %
Rwork0.1215 68253 -
obs0.1239 71845 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 128 498 4784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00464591
X-RAY DIFFRACTIONf_angle_d0.75436301
X-RAY DIFFRACTIONf_chiral_restr0.0757678
X-RAY DIFFRACTIONf_plane_restr0.0055842
X-RAY DIFFRACTIONf_dihedral_angle_d11.7371634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.22421060.13382011X-RAY DIFFRACTION76.68
1.52-1.540.17081220.12262341X-RAY DIFFRACTION86.85
1.54-1.560.17081330.11342512X-RAY DIFFRACTION93.46
1.56-1.590.18091350.11212572X-RAY DIFFRACTION99.01
1.59-1.610.16571410.10932675X-RAY DIFFRACTION99.96
1.61-1.640.1661420.1072707X-RAY DIFFRACTION99.96
1.64-1.660.15931380.10232617X-RAY DIFFRACTION100
1.66-1.690.18551410.122671X-RAY DIFFRACTION99.93
1.69-1.730.18261390.13642656X-RAY DIFFRACTION99.89
1.73-1.760.22151410.12952668X-RAY DIFFRACTION99.86
1.76-1.80.16061410.12182666X-RAY DIFFRACTION99.93
1.8-1.840.20261390.1152658X-RAY DIFFRACTION99.93
1.84-1.890.16321400.10662651X-RAY DIFFRACTION99.96
1.89-1.940.14611410.10442678X-RAY DIFFRACTION99.86
1.94-20.1531400.1112652X-RAY DIFFRACTION99.89
2-2.060.17431400.11162675X-RAY DIFFRACTION100
2.06-2.140.1671390.11512639X-RAY DIFFRACTION99.93
2.14-2.220.15561430.10942719X-RAY DIFFRACTION99.97
2.22-2.320.17831410.11782668X-RAY DIFFRACTION99.89
2.32-2.440.17491400.1192661X-RAY DIFFRACTION99.96
2.44-2.60.15421400.12372662X-RAY DIFFRACTION99.68
2.6-2.80.16481400.1282669X-RAY DIFFRACTION99.47
2.8-3.080.16461410.12842690X-RAY DIFFRACTION99.58
3.08-3.520.15421410.12052682X-RAY DIFFRACTION99.89
3.53-4.440.15161430.11662702X-RAY DIFFRACTION99.75
4.44-47.320.20441450.14762751X-RAY DIFFRACTION99.52

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