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- PDB-2bjh: Crystal Structure Of S133A AnFaeA-ferulic acid complex -

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Basic information

Entry
Database: PDB / ID: 2bjh
TitleCrystal Structure Of S133A AnFaeA-ferulic acid complex
ComponentsFERULOYL ESTERASE A
KeywordsHYDROLASE / DEGRADATION PLANT CELL WALLS / FERULOYL ESTERASE / GLYCOPROTEIN / 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 / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Feruloyl esterase A
Similarity search - Component
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsFaulds, C.B. / Molina, R. / Gonzalez, R. / Husband, F. / Juge, N. / Sanz-Aparicio, J. / Hermoso, J.A.
CitationJournal: FEBS J. / Year: 2005
Title: Probing the Determinants of Substrate Specificity of a Feruloyl Esterase, Anfaea, from Aspergillus Niger
Authors: Faulds, C.B. / Molina, R. / Gonzalez, R. / Husband, F. / Juge, N. / Sanz-Aparicio, J. / Hermoso, J.A.
History
DepositionFeb 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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 2.2Oct 23, 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
C: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,94112
Polymers85,0323
Non-polymers1,9109
Water6,720373
1
A: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9804
Polymers28,3441
Non-polymers6373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9804
Polymers28,3441
Non-polymers6373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: FERULOYL ESTERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9804
Polymers28,3441
Non-polymers6373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.750, 130.750, 76.500
Angle α, β, γ (deg.)90.00, 98.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99999, -0.00166, -0.00393), (0.00172, -0.99989, -0.01502), (-0.0039, -0.01503, 0.99988)23.46257, 94.88925, -0.3918
2given(0.43155, 0.13112, 0.89251), (-0.55936, 0.8151, 0.15072), (-0.70773, -0.56428, 0.4251)-23.78529, 62.56401, 39.55011

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Components

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


Mass: 28343.875 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Strain: CBS 120.49/N400 / Production host: PICHIA PASTORIS (fungus) / 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.: 3
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: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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. ENGINEERED RESIDUE SER 154 ALA, CHAINS A, B AND C. RESIDUE 133 IN THE COORDINATE RECORDS BELOW.
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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growpH: 7.5
Details: 1.7 M AMMONIUM SULPHATE, 0.1 M HEPES, PH = 7.5, [FAXX]= 10 MM.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.918381
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2003 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918381 Å / Relative weight: 1
ReflectionResolution: 2.15→49.5 Å / Num. obs: 47613 / % possible obs: 98.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.9
Reflection shellResolution: 2.41→2.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USW

1usw


Resolution: 2.54→49.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1573406.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1958 6.6 %RANDOM
Rwork0.216 ---
obs0.216 29512 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0691 Å2 / ksol: 0.376446 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--10.66 Å20 Å2-2.06 Å2
2--12.32 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.54→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 132 373 6478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.54→2.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 248 5 %
Rwork0.27 4680 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5FERULATE.PARFERULATE.TOP

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