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- PDB-1uza: Crystallographic structure of a feruloyl esterase from Aspergillu... -

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Basic information

Entry
Database: PDB / ID: 1uza
TitleCrystallographic structure of a feruloyl esterase from Aspergillus niger
ComponentsFERULOYL ESTERASE A
KeywordsHYDROLASE / SERINE ESTERASE / XYLAN DEGRADATION
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: 1.5 Å
AuthorsMcAuley, K.E. / Svendsen, A. / Patkar, S.A. / Wilson, K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of a Feruloyl Esterase from Aspergillus Niger
Authors: Mcauley, K.E. / Svendsen, A. / Patkar, S.A. / Wilson, K.S.
History
DepositionMar 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,5796
Polymers56,9442
Non-polymers6354
Water7,170398
1
A: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7893
Polymers28,4721
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7893
Polymers28,4721
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.298, 39.681, 77.071
Angle α, β, γ (deg.)75.24, 78.82, 71.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 28
2114B1 - 28
1214A35 - 56
2214B35 - 56
1314A60 - 116
2314B60 - 116
1414A127 - 222
2414B127 - 222
1514A224 - 227
2514B224 - 227
1614A233 - 256
2614B233 - 256

NCS oper: (Code: given
Matrix: (0.37556, 0.90163, 0.21453), (0.90091, -0.40948, 0.14382), (0.21752, 0.13926, -0.96607)
Vector: 20.76293, 15.65211, 37.79221)

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Components

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


Mass: 28472.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE AT ASN 79 / Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: O42807, feruloyl esterase
#2: 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.: 2
Source method: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN DEGRADATION OF PLANT CELL WALLS. HYDROLYZES THE FERULOYL-ARABINOSE ESTER BOND IN ...INVOLVED IN DEGRADATION OF PLANT CELL WALLS. HYDROLYZES THE FERULOYL-ARABINOSE ESTER BOND IN ARABINOXYLANS, AND THE FERULOYL-GALACTOSE ESTER BOND IN PECTIN. BINDS TO CELLULOSE. FERULOYL-POLYSACCHARIDE + H(2)O = FERULATE + POLYSACCHARIDE.
Has protein modificationY
Sequence detailsTHE CONFLICT DESCRIBED IN THE SEQADV RECORDS BELOW HAVE BEEN DESCRIBED IN UNIPROT ENTRY O42807 BY ...THE CONFLICT DESCRIBED IN THE SEQADV RECORDS BELOW HAVE BEEN DESCRIBED IN UNIPROT ENTRY O42807 BY JUGE ET AL 2001. PUBMED ID: 12702357

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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: 1.8 Å3/Da / Density % sol: 32 %
Crystal growpH: 4.5 / Details: 1.0 M AMMONIUM SULPHATE, 0.1M NA ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 64076 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 1.51→1.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2.5 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4TGL

4tgl


Resolution: 1.5→74.54 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.314 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3252 5.11 %RANDOM
Rwork0.156 ---
obs0.158 64009 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.131 Å20.122 Å20.318 Å2
2--0.988 Å20.137 Å2
3----1.128 Å2
Refinement stepCycle: LAST / Resolution: 1.5→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 38 398 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214175
X-RAY DIFFRACTIONr_bond_other_d0.0050.023462
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9255711
X-RAY DIFFRACTIONr_angle_other_deg0.96538100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61225.64211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88615621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6281513
X-RAY DIFFRACTIONr_chiral_restr0.1260.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2290.2923
X-RAY DIFFRACTIONr_nbd_other0.2020.23527
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22186
X-RAY DIFFRACTIONr_nbtor_other0.090.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3881.53235
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73224174
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.91531872
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8294.51537
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3169 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.320.5
2Bmedium thermal0.922
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 223
Rwork0.168 4388

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