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Basic information

Entry
Database: PDB / ID: 8jh9
TitleStructure-based characterization and improvement of an enzymatic activity of Acremonium alcalophilum feruloyl esterase
ComponentsFeruloyl esterase with ferulic acid
KeywordsHYDROLASE / Feruloyl esterase
Function / homology3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
Function and homology information
Biological speciesSodiomyces alcalophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Nov 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

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Assembly

Deposited unit
A: Feruloyl esterase with ferulic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6174
Polymers26,9741
Non-polymers6433
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint6 kcal/mol
Surface area10480 Å2
Unit cell
Length a, b, c (Å)101.274, 38.572, 77.878
Angle α, β, γ (deg.)90.000, 125.563, 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-302-

MG

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Components

#1: Protein Feruloyl esterase with ferulic acid


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)
#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: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris-HCl, and 30% (w/v) PEG4,000

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Data collection

DiffractionMean temperature: 293 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: 2→50 Å / Num. obs: 16580 / % possible obs: 97.7 % / Redundancy: 4.21 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.038 / Net I/σ(I): 30.63
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 10.18 / Num. unique obs: 2438 / CC1/2: 0.984 / Rrim(I) all: 0.157 / % possible all: 89.8

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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: 8JH8

8jh8


Resolution: 2→41.19 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1823 829 5 %
Rwork0.132 15749 -
obs0.1344 16578 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.84 Å2
Refinement stepCycle: LAST / Resolution: 2→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 43 133 2017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652068
X-RAY DIFFRACTIONf_angle_d0.7692845
X-RAY DIFFRACTIONf_chiral_restr0.0565292
X-RAY DIFFRACTIONf_plane_restr0.0063393
X-RAY DIFFRACTIONf_dihedral_angle_d14.4955777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.120.1941260.15062394X-RAY DIFFRACTION90.23
2.12-2.290.22511390.13952649X-RAY DIFFRACTION99.57
2.29-2.520.21941380.14142619X-RAY DIFFRACTION100
2.52-2.880.17641410.14862689X-RAY DIFFRACTION99.93
2.88-3.630.20911410.13612671X-RAY DIFFRACTION99.65
3.63-41.190.14311440.11472727X-RAY DIFFRACTION99.07

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