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Basic information

Entry
Database: PDB / ID: 2ix9
TitleRespective role of protein folding and glycosylation in the thermal stability of recombinant Feruloyl Esterase A
ComponentsFERULOYL ESTERASE A
KeywordsHYDROLASE / XYLAN DEGRADATION / FERULOYL ESTERASE EC 3.1.1.73 / GLYCOPROTEIN / SERINE ESTERASE
Function / homology
Function and homology information


feruloyl esterase / feruloyl esterase activity / pectin catabolic process / cellulose binding / xylan catabolic process / cellulose catabolic process / lipid metabolic process / cell wall macromolecule catabolic process / extracellular region
Similarity search - Function
: / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSulzenbacher, G. / Benoit, I.
CitationJournal: FEBS Lett. / Year: 2006
Title: Respective Importance of Protein Folding and Glycosylation in the Thermal Stability of Recombinant Feruloyl Esterase A.
Authors: Benoit, I. / Asther, M. / Sulzenbacher, G. / Record, E. / Marmuse, L. / Parsiegla, G. / Gimbert, I. / Asther, M. / Bignon, C.
History
DepositionJul 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERULOYL ESTERASE A
B: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,87714
Polymers56,7462
Non-polymers1,13112
Water9,458525
1
A: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0018
Polymers28,3731
Non-polymers6287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8776
Polymers28,3731
Non-polymers5045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.825, 51.556, 72.553
Angle α, β, γ (deg.)90.00, 109.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2036-

HOH

21A-2084-

HOH

31A-2087-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.25029, 0.70753, 0.66087), (0.71384, -0.32627, 0.61966), (0.65406, 0.62685, -0.4234)
Vector: -9.98216, -40.47337, 55.38137)

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Components

#1: Protein FERULOYL ESTERASE A / FERULOYL ESTERASE TYPE A / FAE-III / CINNAMOYL ESTERASE


Mass: 28372.918 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 22-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Strain: D15PYRG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O42807, feruloyl esterase
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 9.5
Details: 1.8 M AMMONIUM SULPHATE 0.2 M LITHIUM SULPHATE 0.1 M CAPS PH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→62 Å / Num. obs: 60965 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 14.42 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HL6

2hl6


Resolution: 1.7→74.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.707 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.B FACTORS CORRESPOND TO THE OVERALL B FACTORS EQUAL TO THE RESIDUAL PLUS THE TLS COMPONENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3096 5.1 %RANDOM
Rwork0.153 ---
obs0.155 57868 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20.04 Å2
2---0.44 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 70 525 4583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214241
X-RAY DIFFRACTIONr_bond_other_d0.0020.022698
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9395807
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0046607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76325.714210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27115619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5861512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
X-RAY DIFFRACTIONr_nbd_refined0.2150.2907
X-RAY DIFFRACTIONr_nbd_other0.2030.23015
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22178
X-RAY DIFFRACTIONr_nbtor_other0.0870.22036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.68133385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03844254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99731892
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.83241537
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 208
Rwork0.204 3942
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6534-0.06150.01160.88160.09070.6423-0.00190.05870.0331-0.0335-0.0159-0.055-0.01170.02310.0178-0.0549-0.00260.0119-0.04030.0037-0.04489.1960.33521.952
21.0134-0.1253-0.06950.6926-0.08680.6844-0.0066-0.1173-0.05310.06180.02320.00670.02190.0097-0.0166-0.03620.00750.0061-0.02390.0064-0.05322.446-20.39452.299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 260
2X-RAY DIFFRACTION2B1 - 260

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