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- PDB-2drs: Crystal structure of reducing-end-xylose releasing exo-oligoxylan... -

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Basic information

Entry
Database: PDB / ID: 2drs
TitleCrystal structure of reducing-end-xylose releasing exo-oligoxylanase D263S mutant
ComponentsXylanase Y
KeywordsHYDROLASE / (ALPLA/ALPHA)6 BARREL / GLYCOSIDE HYDROLASE FAMILY 8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


oligosaccharide reducing-end xylanase / oligosaccharide reducing-end xylanase activity / xylan catabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Reducing end xylose-releasing exo-oligoxylanase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsFushinobu, S. / Hidaka, M. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M.
Citation
Journal: J.Biochem. / Year: 2009
Title: Structural explanation for the acquisition of glycosynthase activity
Authors: Hidaka, M. / Fushinobu, S. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: The first glycosynthase derived from an inverting glycoside hydrolase
Authors: Honda, Y. / Kitaoka, M.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125
Authors: Fushinobu, S. / Hidaka, M. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M.
#3: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary X-ray analysis of reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125
Authors: Honda, Y. / Fushinobu, S. / Hidaka, M. / Wakagi, T. / Shoun, H. / Kitaoka, M.
#4: Journal: J.Biol.Chem. / Year: 2004
Title: A family 8 glycoside hydrolase from Bacillus halodurans C-125 (BH2105) is a reducing end xylose-releasing exo-oligoxylanase
Authors: Honda, Y. / Kitaoka, M.
History
DepositionJun 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
A: Xylanase Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2523
Polymers46,1011
Non-polymers1512
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.249, 85.026, 86.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xylanase Y / reducing-end-xylose releasing exo-oligoxylanase


Mass: 46100.793 Da / Num. of mol.: 1 / Mutation: K2E/D263S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2105 / Plasmid: PET28B-BH2105 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3)
References: UniProt: Q9KB30, oligosaccharide reducing-end xylanase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, SODIUM ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Oct 22, 2004
RadiationMonochromator: Triangular Si(111) with an asymmetric angle of 7.8degree
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→60.746 Å / Num. all: 23314 / Num. obs: 22673 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.099 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 2294 / Rsym value: 0.243 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1WU4

1wu4


Resolution: 2.1→43.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.956 / SU ML: 0.109 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21041 1163 5.1 %RANDOM
Rwork0.14013 ---
all0.1437 21506 --
obs0.1437 21506 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.255 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.1788 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 7 431 3544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223215
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9264359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67823.989178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04815492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4091517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21612
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22174
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8481.51937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36723002
X-RAY DIFFRACTIONr_scbond_it2.25231535
X-RAY DIFFRACTIONr_scangle_it3.3914.51357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 79 -
Rwork0.132 1592 -
obs--98.93 %

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