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- PDB-3fyu: Crystal structure of acetyl xylan esterase from Bacillus pumilus ... -

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Basic information

Entry
Database: PDB / ID: 3fyu
TitleCrystal structure of acetyl xylan esterase from Bacillus pumilus obtained in presence of D-xylose and sodium acetate
Components(Acetyl xylan ...) x 3
KeywordsHYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Bacillus pumilus
Function / homology
Function and homology information


acetylesterase / polysaccharide metabolic process / acetylesterase activity
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / beta-D-xylopyranose / Acetyl xylan esterase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.62 Å
AuthorsKrastanova, I. / Cassetta, A. / Lamba, D.
Citation
Journal: To be Published
Title: Structural and functional studies of Bacillus pumilus acetyl xylan esterase
Authors: Krastanova, I. / Cassetta, A. / Mastihubova, M. / Biely, P. / Lamba, D.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: Heterologous expression, purification, crystallization, X-ray analysis and phasing of the acetyl xylan esterase from Bacillus pumilus
Authors: Krastanova, I. / Guarnaccia, C. / Zahariev, S. / Degrassi, G. / Lamba, D.
#2: Journal: Microbiology / Year: 2000
Title: The acetyl xylan esterase of Bacillus pumilus belongs to a family of esterases with broad substrate specificity
Authors: Degrassi, G. / Kojic, M. / Ljubijankic, G. / Venturi, V.
#3: Journal: Appl.Environ.Microbiol. / Year: 1998
Title: Purification and characterization of an acetyl xylan esterase from Bacillus pumilus
Authors: Degrassi, G. / Okeke, B.C. / Bruschi, C.V. / Venturi, V.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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 2.2Nov 22, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl xylan esterase
B: Acetyl xylan esterase
C: Acetyl xylan esterase
D: Acetyl xylan esterase
E: Acetyl xylan esterase
F: Acetyl xylan esterase
G: Acetyl xylan esterase
H: Acetyl xylan esterase
I: Acetyl xylan esterase
L: Acetyl xylan esterase
M: Acetyl xylan esterase
N: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,43955
Polymers433,64212
Non-polymers2,79643
Water14,484804
1
A: Acetyl xylan esterase
B: Acetyl xylan esterase
C: Acetyl xylan esterase
D: Acetyl xylan esterase
E: Acetyl xylan esterase
F: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,29729
Polymers216,8516
Non-polymers1,44623
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21560 Å2
ΔGint-130 kcal/mol
Surface area61730 Å2
MethodPISA
2
G: Acetyl xylan esterase
H: Acetyl xylan esterase
I: Acetyl xylan esterase
L: Acetyl xylan esterase
M: Acetyl xylan esterase
N: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,14126
Polymers216,7916
Non-polymers1,35020
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20970 Å2
ΔGint-147 kcal/mol
Surface area62030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.225, 86.622, 183.973
Angle α, β, γ (deg.)90.000, 112.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Acetyl xylan ... , 3 types, 12 molecules AIBDHCEFGLMN

#1: Protein Acetyl xylan esterase


Mass: 36156.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase
#2: Protein Acetyl xylan esterase


Mass: 36174.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase
#3: Protein
Acetyl xylan esterase


Mass: 36114.844 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase

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Sugars , 1 types, 7 molecules

#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 840 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.3M lithium chloride, 0.2M sodium acetate, 0.2M D-xylose, 5% PEG 6000, 0.05M MES, pH 6.0, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2004
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.62→30 Å / Num. all: 106905 / Num. obs: 106905 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.49 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.136
Reflection shellResolution: 2.62→2.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.3 / Num. unique all: 8208 / Χ2: 1.028 / % possible all: 80.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345controldata collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3FVT

3fvt


Resolution: 2.62→26.88 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 10592 8.5 %RANDOM
Rwork0.196 ---
all0.196 106893 --
obs0.196 106893 86 %-
Solvent computationBsol: 14.674 Å2
Displacement parametersBiso max: 50.86 Å2 / Biso mean: 19.338 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1-6.644 Å20 Å2-4.255 Å2
2---0.171 Å20 Å2
3----6.474 Å2
Refinement stepCycle: LAST / Resolution: 2.62→26.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30418 0 160 804 31382
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.234
X-RAY DIFFRACTIONc_mcbond_it1.0031.5
X-RAY DIFFRACTIONc_scbond_it1.7162
X-RAY DIFFRACTIONc_mcangle_it1.5992
X-RAY DIFFRACTIONc_scangle_it2.5942.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5lig_m2.parlig_m2.top

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