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Basic information

Entry
Database: PDB / ID: 8jh8
TitleStructure-based characterization and improvement of an enzymatic activity of Acremonium alcalophilum feruloyl esterase
ComponentsFeruloyl esterase
KeywordsHYDROLASE / Feruloyl esterase
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesSodiomyces alcalophilus (fungus)
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
CitationJournal: Acs Sustain Chem Eng / Year: 2024
Title: Structure-Based Characterization and Improvement of an Enzymatic Activity of Acremonium alcalophilum Feruloyl Esterase
Authors: Phienluphon, A. / Kondo, K. / Mikami, B. / Teo, K.S.K. / Saito, K. / Watanabe, T. / Nagata, T. / Katahira, M.
History
DepositionMay 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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

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Assembly

Deposited unit
A: Feruloyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5535
Polymers26,9741
Non-polymers5794
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.516, 37.738, 77.709
Angle α, β, γ (deg.)90.000, 125.928, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-303-

MG

21A-614-

HOH

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Components

#1: Protein Feruloyl esterase


Mass: 26974.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sodiomyces alcalophilus (fungus) / Production host: Komagataella pastoris (fungus) / References: feruloyl esterase
#2: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris-HCl, 30% (w/v) PEG4,000

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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 23, 2021
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: 33128 / % possible obs: 95.9 % / Redundancy: 5.23 % / Biso Wilson estimate: 21.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Net I/σ(I): 18.61
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.84 / Num. unique obs: 4350 / CC1/2: 0.875 / Rrim(I) all: 0.345 / % possible all: 95.9

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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: AlphaFold

Resolution: 1.55→37.78 Å / SU ML: 0.2043 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 1657 5 %
Rwork0.1487 31471 -
obs0.1525 33128 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 37 235 2113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481970
X-RAY DIFFRACTIONf_angle_d0.73412685
X-RAY DIFFRACTIONf_chiral_restr0.0534274
X-RAY DIFFRACTIONf_plane_restr0.0058367
X-RAY DIFFRACTIONf_dihedral_angle_d13.9798717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.29031030.22341948X-RAY DIFFRACTION71.79
1.59-1.640.27821220.19862321X-RAY DIFFRACTION85.99
1.64-1.70.28681390.1882638X-RAY DIFFRACTION97.89
1.7-1.770.29341420.1892711X-RAY DIFFRACTION99.93
1.77-1.850.25811410.1742677X-RAY DIFFRACTION100
1.85-1.950.23261440.16772724X-RAY DIFFRACTION100
1.95-2.070.27621420.16162717X-RAY DIFFRACTION99.93
2.07-2.230.24521440.16392727X-RAY DIFFRACTION99.93
2.23-2.460.22731430.15322710X-RAY DIFFRACTION99.93
2.46-2.810.24581430.15622726X-RAY DIFFRACTION99.97
2.81-3.540.20661450.142752X-RAY DIFFRACTION99.45
3.54-37.780.18371490.12322820X-RAY DIFFRACTION99.76

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