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- PDB-8bhh: The crystal structure of a feruloyl esterase C from Fusarium oxys... -

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Basic information

Entry
Database: PDB / ID: 8bhh
TitleThe crystal structure of a feruloyl esterase C from Fusarium oxysporum in complex with p-coumaric acid
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / ferulic acid esterase / coummaric acid / tannase-like / feruloyl esterase
Function / homologyTannase/feruloyl esterase / Tannase and feruloyl esterase / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / 4'-HYDROXYCINNAMIC ACID / DI(HYDROXYETHYL)ETHER / Carboxylic ester hydrolase
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsDimarogona, M. / Topakas, E. / Kosinas, C. / Ferousi, C. / Nikolaivits, E.
Funding support Greece, European Union, 2items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)03061 Greece
European CommissioniNEXT discovery (PID 12346European Union
Citation
Journal: Febs Lett. / Year: 2023
Title: Crystal structure of the Fusarium oxysporum tannase-like feruloyl esterase FaeC in complex with p-coumaric acid provides insight into ligand binding.
Authors: Ferousi, C. / Kosinas, C. / Nikolaivits, E. / Topakas, E. / Dimarogona, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structure-function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role.
Authors: Kosinas, C. / Zerva, A. / Topakas, E. / Dimarogona, M.
History
DepositionOct 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: 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
Revision 1.2Jan 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
B: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,02127
Polymers112,2872
Non-polymers8,73425
Water16,051891
1
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,61210
Polymers56,1441
Non-polymers3,4689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,41017
Polymers56,1441
Non-polymers5,26616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.704, 89.637, 116.978
Angle α, β, γ (deg.)90.00, 103.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carboxylic ester hydrolase


Mass: 56143.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: faeC / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A1D3S5H0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 3 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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
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 , 7 types, 908 molecules

#4: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG400, Tris HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.69→113.51 Å / Num. obs: 105053 / % possible obs: 69.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 1.69→1.835 Å / Num. unique obs: 5255 / CC1/2: 0.594

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAT

6fat


Resolution: 1.69→113.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.564 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 5158 4.9 %RANDOM
Rwork0.17101 ---
obs0.17321 99895 69.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.708 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.26 Å2
2---0.31 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.69→113.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7844 0 581 891 9316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138807
X-RAY DIFFRACTIONr_bond_other_d0.0020.0157819
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.72811907
X-RAY DIFFRACTIONr_angle_other_deg1.4171.64918132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09451029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37422.606426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.849151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9071543
X-RAY DIFFRACTIONr_chiral_restr0.0870.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029683
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022004
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_it2.5582.8064090
X-RAY DIFFRACTIONr_mcbond_other2.5582.8064088
X-RAY DIFFRACTIONr_mcangle_it3.2574.1965120
X-RAY DIFFRACTIONr_mcangle_other3.2574.1975121
X-RAY DIFFRACTIONr_scbond_it3.4163.1354717
X-RAY DIFFRACTIONr_scbond_other3.4163.1354717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8084.5726786
X-RAY DIFFRACTIONr_long_range_B_refined6.04934.60910439
X-RAY DIFFRACTIONr_long_range_B_other6.0534.60910439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.691→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 30 -
Rwork0.29 637 -
obs--5.98 %

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