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- PDB-8bf3: Crystal structure of feruloyl esterase wtsFae1B in complex with x... -

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Basic information

Entry
Database: PDB / ID: 8bf3
TitleCrystal structure of feruloyl esterase wtsFae1B in complex with xylobiose
ComponentsFerulic acid esterase
KeywordsSUGAR BINDING PROTEIN / Feruloyl esterase / complex / (alpha/beta/alpha)-sandwich
Function / homology
Function and homology information


feruloyl esterase / feruloyl esterase activity / acyltransferase activity, transferring groups other than amino-acyl groups / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Esterase-like / Putative esterase / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-xylopyranose / Ferulic acid esterase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsWilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Other government Denmark
CitationJournal: To Be Published
Title: Crystal structure of feruloyl esterase wtsFae1B in complex with xylobiose
Authors: Wilkens, C.
History
DepositionOct 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferulic acid esterase
B: Ferulic acid esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,32918
Polymers86,0272
Non-polymers1,30116
Water18,7901043
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint28 kcal/mol
Surface area26920 Å2
Unit cell
Length a, b, c (Å)65.580, 99.350, 132.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ferulic acid esterase


Mass: 43013.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5S8WFA0, feruloyl esterase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1043 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG6000; 0.1M HEPES pH 7; 0.2M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.19→40.47 Å / Num. obs: 272728 / % possible obs: 98.48 % / Redundancy: 12 % / Biso Wilson estimate: 14.07 Å2 / CC1/2: 1 / Net I/σ(I): 17.57
Reflection shellResolution: 1.19→1.23 Å / Num. unique obs: 177374 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBE3data collection
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BBP

8bbp


Resolution: 1.19→40.47 Å / SU ML: 0.1154 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 13.8599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1377 5520 1.05 %
Rwork0.1167 522668 -
obs0.1169 272728 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.32 Å2
Refinement stepCycle: LAST / Resolution: 1.19→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5443 0 85 1043 6571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585939
X-RAY DIFFRACTIONf_angle_d0.88368065
X-RAY DIFFRACTIONf_chiral_restr0.0754847
X-RAY DIFFRACTIONf_plane_restr0.00831056
X-RAY DIFFRACTIONf_dihedral_angle_d11.9532193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20.33291510.290614519X-RAY DIFFRACTION81.78
1.2-1.220.24421620.278515237X-RAY DIFFRACTION85.96
1.22-1.230.33731670.270615883X-RAY DIFFRACTION89.71
1.23-1.250.27811750.256816869X-RAY DIFFRACTION94.93
1.25-1.260.27911800.250416989X-RAY DIFFRACTION95.32
1.26-1.280.27471850.241917316X-RAY DIFFRACTION97.65
1.28-1.30.22691830.224117654X-RAY DIFFRACTION99.64
1.3-1.320.23971890.201117737X-RAY DIFFRACTION99.93
1.32-1.340.19451890.182617819X-RAY DIFFRACTION99.99
1.34-1.360.17791860.167317734X-RAY DIFFRACTION100
1.36-1.390.16681890.157417731X-RAY DIFFRACTION99.93
1.39-1.410.1561850.141617700X-RAY DIFFRACTION99.98
1.41-1.440.14841890.134917803X-RAY DIFFRACTION99.97
1.44-1.470.14681920.125217751X-RAY DIFFRACTION99.96
1.47-1.50.1331890.115617734X-RAY DIFFRACTION99.97
1.5-1.530.13241880.107317717X-RAY DIFFRACTION99.94
1.53-1.570.13241870.095917741X-RAY DIFFRACTION99.99
1.57-1.620.1111890.088317744X-RAY DIFFRACTION99.97
1.62-1.660.11111870.086717800X-RAY DIFFRACTION99.99
1.66-1.720.10331930.086317745X-RAY DIFFRACTION99.97
1.72-1.780.11081900.08417753X-RAY DIFFRACTION100
1.78-1.850.11611840.089617742X-RAY DIFFRACTION99.99
1.85-1.930.11931900.091417754X-RAY DIFFRACTION99.91
1.93-2.030.12831870.087517738X-RAY DIFFRACTION99.98
2.03-2.160.10751820.093217778X-RAY DIFFRACTION99.98
2.16-2.330.11011820.093317729X-RAY DIFFRACTION99.93
2.33-2.560.13891900.098417737X-RAY DIFFRACTION100
2.56-2.930.11991920.107117754X-RAY DIFFRACTION99.97
2.93-3.70.13241850.110617751X-RAY DIFFRACTION99.98
3.7-40.470.13571830.126817709X-RAY DIFFRACTION99.65

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