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

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Basic information

Entry
Database: PDB / ID: 3wkx
TitleCrystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum arabinose complex 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 / carbohydrate metabolic process
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
beta-L-arabinofuranose / Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6733
Polymers74,4581
Non-polymers2162
Water4,720262
1
A: Non-reducing end beta-L-arabinofuranosidase
hetero molecules

A: Non-reducing end beta-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3476
Polymers148,9162
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5880 Å2
ΔGint-7 kcal/mol
Surface area43900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.726, 77.726, 252.668
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-958-

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: pET-23b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3)
References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase
#2: Sugar ChemComp-FUB / beta-L-arabinofuranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArafbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinofuranoseCOMMON NAMEGMML 1.0
b-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.7M sodium citrate, 0.1M MES, 10mM DTT, 20% L-arabinose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2012
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: 2→50 Å / Num. all: 68980 / Num. obs: 59588 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rsym value: 0.06 / Net I/σ(I): 43
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2994 / Rsym value: 0.693 / % possible all: 98.6

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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: FOURIER SYNTHESIS / Resolution: 2→29.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.006 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27871 2892 5 %RANDOM
Rwork0.22635 ---
obs0.22902 54418 93.87 %-
all-57972 --
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: 41.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.183 Å0.191 Å
Luzzati sigma a-0.155 Å
Refinement stepCycle: LAST / Resolution: 2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 11 262 5413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195271
X-RAY DIFFRACTIONr_bond_other_d0.0020.024825
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9467169
X-RAY DIFFRACTIONr_angle_other_deg0.9193.00111079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9924.135266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72615819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9351536
X-RAY DIFFRACTIONr_chiral_restr0.110.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021248
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: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 206 -
Rwork0.355 4063 -
obs--96.54 %

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