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- PDB-8bbp: Crystal structure of feruloyl esterase wtsFae1B -

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Basic information

Entry
Database: PDB / ID: 8bbp
TitleCrystal structure of feruloyl esterase wtsFae1B
Components(Ferulic acid esterase) x 2
KeywordsRECOMBINATION / esterase / dimer / (alpha/beta/alpha)-sandwich
Function / homology
Function and homology information


feruloyl esterase / feruloyl esterase activity / 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
Ferulic acid esterase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsWilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of feruloyl esterase wtsFae1B
Authors: Wilkens, C.
History
DepositionOct 14, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,37924
Polymers86,0132
Non-polymers1,36522
Water20,7711153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint51 kcal/mol
Surface area27180 Å2
Unit cell
Length a, b, c (Å)65.320, 132.510, 98.830
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.: 1
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: Protein Ferulic acid esterase


Mass: 42999.594 Da / Num. of mol.: 1
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
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 294 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: 0.65 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 1.07→49.41 Å / Num. obs: 377200 / % possible obs: 99.7 % / Redundancy: 13.63 % / Biso Wilson estimate: 12.49 Å2 / CC1/2: 1 / Net I/σ(I): 1.03
Reflection shellResolution: 1.07→1.12 Å / Num. unique obs: 59686 / CC1/2: 0.49

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZN

6rzn


Resolution: 1.07→33.13 Å / SU ML: 0.1097 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.4647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1364 3959 1.05 %
Rwork0.122 373182 -
obs0.1221 377141 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.75 Å2
Refinement stepCycle: LAST / Resolution: 1.07→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 88 1153 6697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616034
X-RAY DIFFRACTIONf_angle_d0.90718185
X-RAY DIFFRACTIONf_chiral_restr0.0748855
X-RAY DIFFRACTIONf_plane_restr0.00871074
X-RAY DIFFRACTIONf_dihedral_angle_d16.6522258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.080.33821290.336812157X-RAY DIFFRACTION91.84
1.08-1.090.2961410.29413257X-RAY DIFFRACTION99.98
1.09-1.110.25781410.269313319X-RAY DIFFRACTION99.96
1.11-1.120.24961400.251613202X-RAY DIFFRACTION99.98
1.12-1.140.24631410.239613296X-RAY DIFFRACTION99.96
1.14-1.160.2461410.227413218X-RAY DIFFRACTION99.96
1.16-1.170.24781410.21413314X-RAY DIFFRACTION99.97
1.17-1.190.22921410.212813262X-RAY DIFFRACTION99.99
1.19-1.210.22651410.194713291X-RAY DIFFRACTION100
1.21-1.240.21341410.181913293X-RAY DIFFRACTION99.99
1.24-1.260.17861410.165513324X-RAY DIFFRACTION99.99
1.26-1.290.17241400.152313297X-RAY DIFFRACTION99.99
1.29-1.310.16651410.13913265X-RAY DIFFRACTION100
1.31-1.340.16021420.131613343X-RAY DIFFRACTION99.99
1.34-1.380.14091410.123113322X-RAY DIFFRACTION99.99
1.38-1.420.1331410.115213314X-RAY DIFFRACTION99.99
1.42-1.460.14141420.10913335X-RAY DIFFRACTION100
1.46-1.50.11691410.094713334X-RAY DIFFRACTION99.99
1.5-1.560.10541420.085513378X-RAY DIFFRACTION99.99
1.56-1.620.10661420.084913350X-RAY DIFFRACTION99.97
1.62-1.690.12231420.08713365X-RAY DIFFRACTION99.98
1.69-1.780.11571420.090313376X-RAY DIFFRACTION99.99
1.78-1.890.10651420.093313438X-RAY DIFFRACTION99.99
1.89-2.040.11621430.090313482X-RAY DIFFRACTION99.99
2.04-2.250.10871430.09313469X-RAY DIFFRACTION100
2.25-2.570.10791440.102613515X-RAY DIFFRACTION100
2.57-3.240.12761440.117113635X-RAY DIFFRACTION100
3.24-33.130.13321490.129614031X-RAY DIFFRACTION99.92

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