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- PDB-3fyt: Crystal structure of Bacillus pumilus acetyl xylan esterase S181A... -

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Basic information

Entry
Database: PDB / ID: 3fyt
TitleCrystal structure of Bacillus pumilus acetyl xylan esterase S181A mutant in complex with beta-D-xylopyranose
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Bacillus pumilus
Function / homology
Function and homology information


acetylesterase / 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
beta-D-xylopyranose / Acetyl xylan esterase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.58 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)435,29252
Polymers433,18612
Non-polymers2,10640
Water6,521362
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)217,79627
Polymers216,5936
Non-polymers1,20321
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19520 Å2
ΔGint-242 kcal/mol
Surface area64230 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)217,49625
Polymers216,5936
Non-polymers90319
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-235 kcal/mol
Surface area64340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.186, 167.986, 144.471
Angle α, β, γ (deg.)90.000, 91.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyl xylan esterase


Mass: 36098.844 Da / Num. of mol.: 12 / Mutation: S181A
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: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Cl
#3: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.20M lithium chloride, 0.13M D-xylose, 3% PEG 6000, 0.03M MES, pH 6.0, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.58→24.83 Å / Num. all: 100895 / Num. obs: 100895 / % possible obs: 77.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.66 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.117
Reflection shellResolution: 2.58→2.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / Num. unique all: 4985 / Χ2: 1.021 / % possible all: 50.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3fvr


Resolution: 2.58→24.83 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 10126 7.8 %RANDOM
Rwork0.188 ---
all0.188 100895 --
obs0.188 100895 77.4 %-
Solvent computationBsol: 39.298 Å2
Displacement parametersBiso max: 100 Å2 / Biso mean: 28.857 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1--0.891 Å20 Å2-4.864 Å2
2--6.451 Å20 Å2
3----5.56 Å2
Refinement stepCycle: LAST / Resolution: 2.58→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30044 0 94 362 30500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.207
X-RAY DIFFRACTIONc_mcbond_it4.8621.5
X-RAY DIFFRACTIONc_scbond_it7.8192
X-RAY DIFFRACTIONc_mcangle_it6.5232
X-RAY DIFFRACTIONc_scangle_it9.7362.5
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 DIFFRACTION5xyp.parxyp.top

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