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- PDB-4oap: An Axe2 mutant (W190I), an acetyl-xylooligosaccharide esterase fr... -

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Basic information

Entry
Database: PDB / ID: 4oap
TitleAn Axe2 mutant (W190I), an acetyl-xylooligosaccharide esterase from Geobacillus Stearmophilus
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / SGNH fold
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
ACETATE ION / Acetylxylan esterase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLansky, S. / Alalouf, O. / Solomon, H.V. / Belrhali, H. / Shoham, Y. / Shoham, G.
CitationJournal: To be Published
Title: An Axe2 mutant (W190I), an acetyl-xylooligosaccharide esterase from Geobacillus Stearmophilus
Authors: Lansky, S. / Alalouf, O. / Solomon, H.V. / Belrhali, H. / Shoham, Y. / Shoham, G.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)50,62417
Polymers49,4552
Non-polymers1,16915
Water7,782432
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)202,49668
Polymers197,8208
Non-polymers4,67660
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 area33210 Å2
ΔGint-266 kcal/mol
Surface area60470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.950, 109.950, 213.342
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-426-

HOH

21A-476-

HOH

31B-405-

HOH

41B-441-

HOH

51B-541-

HOH

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Components

#1: Protein Acetyl xylan esterase


Mass: 24727.477 Da / Num. of mol.: 2 / Mutation: W190I
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.4M potassium sodium tartrate, 0.1M imidazole buffer, pH 7.8, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2012
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→35 Å / Num. all: 46932 / Num. obs: 46932 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.93→1.96 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3W7V

3w7v


Resolution: 1.93→34.79 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.561 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 2503 5.1 %RANDOM
Rwork0.14626 ---
obs0.14794 46932 100 %-
all-46932 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.975 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--1.45 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 74 432 3984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193675
X-RAY DIFFRACTIONr_bond_other_d0.0010.023597
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.9774970
X-RAY DIFFRACTIONr_angle_other_deg0.98338264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90123.452168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3215642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6241531
X-RAY DIFFRACTIONr_chiral_restr0.1420.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 181 -
Rwork0.189 3403 -
obs--99.67 %

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