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- PDB-1uwc: Feruloyl esterase from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 1uwc
TitleFeruloyl 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
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Feruloyl esterase A
Similarity search - Component
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.08 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
DepositionFeb 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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

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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)58,1619
Polymers56,9442
Non-polymers1,2177
Water12,845713
1
A: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2746
Polymers28,4721
Non-polymers8025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8873
Polymers28,4721
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.759, 40.182, 77.953
Angle α, β, γ (deg.)74.96, 78.63, 71.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.376, 0.902, 0.213), (0.902, -0.409, 0.138), (0.212, 0.141, -0.967)
Vector: 21.11, 15.88, 38.18)

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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


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-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H10O4
#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.: 713 / 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.
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

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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: 1.0M AMMONIUM SULPHATE, 0.1M NA ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.08→25 Å / Num. obs: 170583 / % possible obs: 93.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.8
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.5 / % possible all: 82

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
ACORNphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.08→74.54 Å / SU B: 0.778 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027
RfactorNum. reflection% reflectionSelection details
Rfree0.13802 8620 5.1 %RANDOM
Rwork0.11511 ---
obs0.116 161840 93 %-
Displacement parametersBiso mean: 9.012 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0.36 Å20.26 Å2
2--0.63 Å2-0.09 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.08→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 80 713 4789

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