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- PDB-3a3v: Crystal structure of reducing-end-xylose releasing exo-oligoxylan... -

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Basic information

Entry
Database: PDB / ID: 3a3v
TitleCrystal structure of reducing-end-xylose releasing exo-oligoxylanase Y198F mutant
ComponentsXylanase Y
KeywordsHYDROLASE / Xylan degradation
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsHidaka, M. / Fushinobu, S. / Honda, Y. / Kitaoka, M.
Citation
Journal: J.Biochem. / Year: 2010
Title: Structural explanation for the acquisition of glycosynthase activity
Authors: Hidaka, M. / Fushinobu, S. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M.
#1: Journal: Glycobiology / Year: 2008
Title: Alternative strategy for converting an inverting glycoside hydrolase into a glycosynthase
Authors: Honda, Y. / Fushinobu, S. / Hidaka, M. / Wakagi, T. / Shoun, H. / Taniguchi, H. / Kitaoka, M.
#2: Journal: J.Biol.Chem. / Year: 2006
Title: The first glycosynthase derived from an inverting glycoside hydrolase
Authors: Honda, Y. / Kitaoka, M.
#3: 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.
#4: 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.
#5: 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 22, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 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)46,5406
Polymers46,1131
Non-polymers4275
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.191, 86.207, 87.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46112.801 Da / Num. of mol.: 1 / Mutation: K2E,Y198F
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 BL21 (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 43.6 %
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: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2007
RadiationMonochromator: Numerical link type Si(111)double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. all: 81959 / Num. obs: 81761 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.1
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.5 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WU4

1wu4


Resolution: 1.39→45.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.888 / SU R Cruickshank DPI: 0.06 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4098 5 %RANDOM
Rwork0.177 ---
obs0.178 81677 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.25 Å2 / Biso mean: 14.73 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.1439 Å
Refinement stepCycle: LAST / Resolution: 1.39→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 25 516 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223208
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9294344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13424.022179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82915486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0551517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212581
X-RAY DIFFRACTIONr_mcbond_it0.5961.51866
X-RAY DIFFRACTIONr_mcangle_it1.10222976
X-RAY DIFFRACTIONr_scbond_it1.64131342
X-RAY DIFFRACTIONr_scangle_it2.5284.51368
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 307 -
Rwork0.259 5624 -
all-5931 -
obs--99.25 %

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