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- PDB-5bn1: Structure of Axe2-W215I, an acetyl xylan esterase from Geobacillu... -

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Basic information

Entry
Database: PDB / ID: 5bn1
TitleStructure of Axe2-W215I, an acetyl xylan esterase from Geobacillus stearothermophilus
ComponentsAcetyl xylan esterase
KeywordsHYDROLASE / acetyl xylan esterase / octamer / mutant / SGNH
Function / homology
Function and homology information


acetylxylan esterase / acetylxylan esterase 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
IMIDAZOLE / Acetylxylan esterase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLansky, S. / Alalouf, O. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
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. / Belrahli, H. / Shoham, Y. / Shoham, G.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)50,10911
Polymers49,4552
Non-polymers6549
Water9,998555
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)200,43444
Polymers197,8208
Non-polymers2,61436
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 area28050 Å2
ΔGint-167 kcal/mol
Surface area59540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.880, 108.880, 216.120
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-411-

HOH

21A-504-

HOH

31A-605-

HOH

41A-615-

HOH

51B-487-

HOH

61B-611-

HOH

71B-677-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetyl xylan esterase


Mass: 24727.477 Da / Num. of mol.: 2 / Mutation: W215I
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

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Non-polymers , 5 types, 564 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.2 M K tartrate, 0.3 M NaCl, 0.1 M imidazole buffer pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 85395 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w7v

3w7v


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.111 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16577 4272 5 %RANDOM
Rwork0.14399 ---
obs0.14511 81089 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 42 555 4053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0193637
X-RAY DIFFRACTIONr_bond_other_d0.0010.023552
X-RAY DIFFRACTIONr_angle_refined_deg2.671.9734932
X-RAY DIFFRACTIONr_angle_other_deg1.13138161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2723.614166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4941529
X-RAY DIFFRACTIONr_chiral_restr0.170.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
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_it2.0841.7961767
X-RAY DIFFRACTIONr_mcbond_other2.0761.7921765
X-RAY DIFFRACTIONr_mcangle_it2.6962.6842210
X-RAY DIFFRACTIONr_mcangle_other2.6952.6862211
X-RAY DIFFRACTIONr_scbond_it4.0762.1491870
X-RAY DIFFRACTIONr_scbond_other4.0742.1491870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6413.0652711
X-RAY DIFFRACTIONr_long_range_B_refined7.82616.8684756
X-RAY DIFFRACTIONr_long_range_B_other7.82616.874757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 326 -
Rwork0.239 5886 -
obs--99.97 %

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