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

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Basic information

Entry
Database: PDB / ID: 2dro
TitleCrystal structure of reducing-end-xylose releasing exo-oligoxylanase D263C 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: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Xylanase Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3604
Polymers46,1171
Non-polymers2433
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.242, 86.369, 87.653
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: 46116.855 Da / Num. of mol.: 1 / Mutation: K2E/D263C
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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2005
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→61.546 Å / Num. all: 45145 / Num. obs: 44431 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 27.45
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 4438 / Rsym value: 0.358 / % possible all: 99.6

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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: 1.7→39.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.646 / SU ML: 0.056 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18731 2252 5.1 %RANDOM
Rwork0.16103 ---
all0.1623 42177 --
obs0.1623 42177 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.1498 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 13 445 3541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9274333
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5095375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9623.989178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9841517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022578
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21588
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22181
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7581.51910
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2422976
X-RAY DIFFRACTIONr_scbond_it2.06331525
X-RAY DIFFRACTIONr_scangle_it3.3034.51357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 174 -
Rwork0.214 3087 -
obs--98.7 %

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