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- PDB-3wkw: Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from... -

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Basic information

Entry
Database: PDB / ID: 3wkw
TitleCrystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum ligand free form
ComponentsNon-reducing end beta-L-arabinofuranosidase
KeywordsHYDROLASE / (alpha/alpha)6 barrel / Intracellular
Function / homology
Function and homology information


non-reducing end beta-L-arabinofuranosidase / beta-L-arabinofuranosidase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function
: / : / Glycoside hydrolase family 127 C-terminal domain / Beta-L-arabinofuranosidase, GH127 / : / Beta-L-arabinofuranosidase, GH127 catalytic domain / Beta-L-arabinofuranosidase, GH127 middle domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsIto, T. / Saikawa, K. / Arakawa, T. / Wakagi, T. / Fujita, K.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum.
Authors: Ito, T. / Saikawa, K. / Kim, S. / Fujita, K. / Ishiwata, A. / Kaeothip, S. / Arakawa, T. / Wakagi, T. / Beckham, G.T. / Ito, Y. / Fushinobu, S.
#1: Journal: J.Biol.Chem. / Year: 2014
Title: Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member
Authors: Fujita, K. / Takashi, Y. / Obuchi, E. / Kitahara, K. / Suganuma, T.
History
DepositionNov 1, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-reducing end beta-L-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)74,4581
Polymers74,4581
Non-polymers00
Water4,143230
1
A: Non-reducing end beta-L-arabinofuranosidase

A: Non-reducing end beta-L-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)148,9162
Polymers148,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5780 Å2
ΔGint-4 kcal/mol
Surface area44860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.833, 75.833, 253.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

21A-883-

HOH

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Components

#1: Protein Non-reducing end beta-L-arabinofuranosidase / Beta-L-arabinofuranosidase HypBA1


Mass: 74457.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: JCM 1217 / Gene: hypBA1 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3)
References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.9M sodium citrate, 0.1 M Na-cacodylate, pH 6.5, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2011
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 44113 / Num. obs: 44051 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rsym value: 0.075 / Net I/σ(I): 36.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 4339 / Rsym value: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→40.09 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.031 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24492 2188 5 %RANDOM
Rwork0.1954 ---
obs0.19789 41349 98.68 %-
all-41902 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.05 Å20 Å2
2--0.05 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.196 Å0.222 Å
Luzzati sigma a-0.148 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 0 230 5236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195121
X-RAY DIFFRACTIONr_bond_other_d0.0020.024709
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9456958
X-RAY DIFFRACTIONr_angle_other_deg0.868310807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72824.077260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04815806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0491536
X-RAY DIFFRACTIONr_chiral_restr0.1060.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215932
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021216
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 163 -
Rwork0.301 2954 -
obs--97.35 %

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