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- PDB-4jj6: Crystal structure of a catalytic mutant of Axe2 (Axe2-H194A), an ... -

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Basic information

Entry
Database: PDB / ID: 4jj6
TitleCrystal structure of a catalytic mutant of Axe2 (Axe2-H194A), 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 A1 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
Acetylxylan esterase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLansky, S. / Alalouf, O. / Solomon, V. / Alhassid, A. / Belrahli, H. / Govada, L. / Chayan, N.E. / Shoham, Y. / Shoham, G.
CitationJournal: To be published
Title: To be published
Authors: Lansky, S. / Alalouf, O. / Solomon, V. / Alhassid, A. / Belrahli, H. / Govada, L. / Chayan, N.E. / Shoham, Y. / Shoham, G.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 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)49,9989
Polymers49,4672
Non-polymers5317
Water8,989499
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)199,99336
Polymers197,8688
Non-polymers2,12628
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 area26000 Å2
ΔGint-251 kcal/mol
Surface area61260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.032, 110.032, 213.135
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-631-

HOH

21A-635-

HOH

31A-636-

HOH

41A-639-

HOH

51B-410-

HOH

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Components

#1: Protein Acetyl xylan esterase


Mass: 24733.459 Da / Num. of mol.: 2 / Mutation: H194A
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.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0-1.4 M K/Na tartrate, 0.3 M NaCl, 0.1 M imidazole buffer, pH 7.0, 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: 1.8→29.86 Å / Num. all: 60800 / Num. obs: 60764 / % possible obs: 99.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.846 Å / % possible all: 99.92

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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: 1.8→29.86 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1802 / WRfactor Rwork: 0.1436 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8718 / SU B: 2.301 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0857 / SU Rfree: 0.0905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 3081 5.1 %RANDOM
Rwork0.1492 ---
obs0.1511 60764 99.92 %-
all-60800 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.6 Å2 / Biso mean: 32.9124 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å20 Å2
2--1.49 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 32 499 4011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193651
X-RAY DIFFRACTIONr_bond_other_d0.0010.023559
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9694951
X-RAY DIFFRACTIONr_angle_other_deg1.00838179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62923.491169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61415642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8111531
X-RAY DIFFRACTIONr_chiral_restr0.1410.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 255 -
Rwork0.28 4163 -
all-4418 -
obs--99.71 %

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