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- PDB-2hl6: Structure of homologously expressed Ferrulate esterase of Aspergi... -

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Basic information

Entry
Database: PDB / ID: 2hl6
TitleStructure of homologously expressed Ferrulate esterase of Aspergillus niger in complex with CAPS
ComponentsFeruloyl esterase A
KeywordsHYDROLASE / Esterase / a/b hydrolase fold / glycosylated / CAPS
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: 1.55 Å
AuthorsParsiegla, G. / Herpoel-Gimbert, I. / Dubots, J.
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. / Herpoel-Gimbert, I. / Asther, M. / Bignon, C.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,56718
Polymers56,7462
Non-polymers2,82116
Water11,115617
1
A: Feruloyl esterase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8217
Polymers28,3731
Non-polymers1,4486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Feruloyl esterase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,74511
Polymers28,3731
Non-polymers1,37210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.520, 51.700, 99.588
Angle α, β, γ (deg.)90.000, 127.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Feruloyl esterase A / Ferulic acid esterase A / FAE-III / Cinnamoyl esterase / Ferrulate esterase A


Mass: 28372.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: faeA / Plasmid: pAN52.3 / Production host: Aspergillus niger (mold) / References: UniProt: O42807, feruloyl esterase

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 631 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 2.05M Ammoniumsulfate, 0.09M CAPS, 10% Ethyleneglycol , pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.934 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 12, 2003
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.55→39.21 Å / Num. all: 227158 / Num. obs: 81359 / % possible obs: 48.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 15.095 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 6.2
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.1 / Num. measured all: 30033 / Num. unique all: 11375 / Rsym value: 0.347 / % possible all: 46.3

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Phasing

Phasing MRRfactor: 0.55 / Cor.coef. Fo:Fc: 0.097 / Cor.coef. Io to Ic: 0.108
Highest resolutionLowest resolution
Rotation3.5 Å20 Å
Translation3.5 Å8 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TGL

3tgl


Resolution: 1.55→39.21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.169 / SU B: 2.433 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4079 5 %RANDOM
Rwork0.163 ---
all0.165 227158 --
obs0.165 81358 96.03 %-
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: 13.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.61 Å2
2---0.13 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 180 617 4785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214345
X-RAY DIFFRACTIONr_bond_other_d0.0020.022739
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.975947
X-RAY DIFFRACTIONr_angle_other_deg0.9343.0046692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39325.61205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60115616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6591512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02830
X-RAY DIFFRACTIONr_nbd_refined0.2150.2937
X-RAY DIFFRACTIONr_nbd_other0.1980.23022
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22242
X-RAY DIFFRACTIONr_nbtor_other0.0910.22077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2450
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0760.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.236
X-RAY DIFFRACTIONr_mcbond_it1.0921.53366
X-RAY DIFFRACTIONr_mcbond_other0.2231.51068
X-RAY DIFFRACTIONr_mcangle_it1.31624241
X-RAY DIFFRACTIONr_scbond_it2.36432010
X-RAY DIFFRACTIONr_scangle_it3.4254.51696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.590.2182750.1845264601692.071
1.59-1.6340.222730.1765354609792.291
1.634-1.6810.212790.1765211591792.784
1.681-1.7330.2062640.1695098573293.545
1.733-1.7890.2132380.1685022558994.113
1.789-1.8520.2022750.1644826539494.568
1.852-1.9220.1962400.1634716518795.547
1.922-20.2022410.1624593501396.429
2-2.0890.1942610.1614444483497.331
2.089-2.190.1772100.1544281457898.1
2.19-2.3080.1612070.1554115437198.879
2.308-2.4480.2022010.153933416199.351
2.448-2.6160.1971860.1593699390899.411
2.616-2.8250.2071670.1673434362899.256
2.825-3.0930.1991770.1653192339499.263
3.093-3.4550.2041570.1622847303598.979
3.455-3.9850.1761480.1512526270998.708
3.985-4.8670.181190.1492131229697.997
4.867-6.8310.2121090.191645179697.661
6.831-39.2230.233520.22948106693.809
Refinement TLS params.Method: refined / Origin x: 56.7851 Å / Origin y: 8.9399 Å / Origin z: 33.8177 Å
111213212223313233
T-0.0162 Å2-0.0013 Å20.0057 Å2--0.0109 Å20.0012 Å2---0.0027 Å2
L0.0692 °2-0.0006 °20.0714 °2-0.0691 °20.0848 °2--0.2855 °2
S0.0097 Å °0.0096 Å °-0.0042 Å °-0.003 Å °0.0037 Å °-0.0085 Å °-0.0036 Å °0.0381 Å °-0.0134 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth seq-ID: 1 - 260 / Label seq-ID: 1 - 260

IDAuth asym-IDLabel asym-ID
1AA
2BB

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