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- PDB-4jko: Crystal structure of a catalytic mutant of Axe2 (Axe2_S15A), an a... -

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Basic information

Entry
Database: PDB / ID: 4jko
TitleCrystal structure of a catalytic mutant of Axe2 (Axe2_S15A), an acetylxylan esterase from Geobacillus stearothermophilus
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / SGNH hydrolase fold / Acetylxylan Esterase / Catalytic mutant
Function / homology
Function and homology information


acetylxylan esterase / acetylxylan esterase activity / phosphatidylcholine lysophospholipase activity / xylan catabolic process / cytoplasm
Similarity search - Function
: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Acetylxylan esterase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAzulay, D. / Lansky, S. / Alalouf, O. / Solomon, V. / Alhassid, A. / Belrahli, H. / Govada, L. / Chayan, N.E. / Shoham, Y. / Shoham, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus.
Authors: Lansky, S. / Alalouf, O. / Solomon, H.V. / Alhassid, A. / Govada, L. / Chayen, N.E. / Belrhali, H. / Shoham, Y. / Shoham, G.
History
DepositionMar 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,49912
Polymers49,5692
Non-polymers93010
Water9,422523
1
A: Acetyl xylan esterase
B: Acetyl xylan esterase
hetero molecules

A: Acetyl xylan esterase
B: Acetyl xylan esterase
hetero molecules

A: Acetyl xylan esterase
B: Acetyl xylan esterase
hetero molecules

A: Acetyl xylan esterase
B: Acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,99548
Polymers198,2768
Non-polymers3,71840
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30810 Å2
ΔGint-242 kcal/mol
Surface area59600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.941, 109.941, 213.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

21A-649-

HOH

31B-417-

HOH

41B-514-

HOH

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Components

#1: Protein Acetyl xylan esterase


Mass: 24784.527 Da / Num. of mol.: 2 / Mutation: S15A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: axe2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09LX1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.25 M NaH2PO4/1.0 M K2HPO4, 0.1 M imidazole buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→34.79 Å / Num. all: 54266 / Num. obs: 51640 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 %
Reflection shellResolution: 1.9→1.948 Å / % possible all: 99.75

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1856 / WRfactor Rwork: 0.1438 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8807 / SU B: 2.678 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1022 / SU Rfree: 0.1055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2626 5.1 %RANDOM
Rwork0.1488 ---
obs0.1508 51640 99.75 %-
all-54266 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.15 Å2 / Biso mean: 32.4848 Å2 / Biso min: 14.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0 Å20 Å2
2--1.75 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 57 523 4068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193662
X-RAY DIFFRACTIONr_bond_other_d0.0010.023558
X-RAY DIFFRACTIONr_angle_refined_deg2.1351.9724960
X-RAY DIFFRACTIONr_angle_other_deg0.96938172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31823.413167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57415636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.371530
X-RAY DIFFRACTIONr_chiral_restr0.1310.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02839
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 170 -
Rwork0.265 3521 -
all-3691 -
obs--97.83 %

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