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- PDB-7dif: GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with... -

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Basic information

Entry
Database: PDB / ID: 7dif
TitleGH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution
ComponentsNon-reducing end beta-L-arabinofuranosidase
KeywordsHYDROLASE / (alpha/alpha)6 barrel / glycoside hydrolase family 127
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
Chem-FE0 / : / Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAmaki, S. / McGregor, N.G.S. / Arakawa, T. / Yamada, C. / Borlandelli, V. / Overkleeft, H.S. / Davies, G.J. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H02443 Japan
Japan Society for the Promotion of Science (JSPS)26660083 Japan
Japan Society for the Promotion of Science (JSPS)19H00929 Japan
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Authors: McGregor, N.G.S. / Coines, J. / Borlandelli, V. / Amaki, S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Yamada, C. / Arakawa, T. / Ishiwata, A. / Ito, Y. / van der Marel, G.A. / Codee, J.D.C. ...Authors: McGregor, N.G.S. / Coines, J. / Borlandelli, V. / Amaki, S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Yamada, C. / Arakawa, T. / Ishiwata, A. / Ito, Y. / van der Marel, G.A. / Codee, J.D.C. / Fushinobu, S. / Overkleeft, H.S. / Rovira, C. / Davies, G.J.
#1: 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.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.5Mar 12, 2025Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,7114
Polymers74,4581
Non-polymers2533
Water4,197233
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)149,4218
Polymers148,9162
Non-polymers5056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area5780 Å2
ΔGint-3 kcal/mol
Surface area43190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.714, 77.714, 252.094
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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 / Fragment: glycoside hydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b) (bacteria)
Strain: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b
Gene: hypBA1, BLLJ_0211 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE0 / (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol


Mass: 148.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES-NaOH (pH 6.5), 0.7 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2020
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.05 Å / Num. obs: 90295 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 10.1 % / Rmerge(I) obs: 3.325 / Num. unique obs: 4409 / CC1/2: 0.67 / Rpim(I) all: 1.527 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKX

3wkx


Resolution: 1.75→46.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 4482 5 %RANDOM
Rwork0.2162 ---
obs0.2176 85691 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.17 Å2 / Biso mean: 42.661 Å2 / Biso min: 28.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.64 Å2-0 Å2
2--1.27 Å20 Å2
3----4.12 Å2
Refinement stepCycle: final / Resolution: 1.75→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 12 233 5381
Biso mean--39.88 43.04 -
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135268
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174789
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6457167
X-RAY DIFFRACTIONr_angle_other_deg2.3681.58311008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32522.45302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16815819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.121536
X-RAY DIFFRACTIONr_chiral_restr0.0740.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026105
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021247
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 318 -
Rwork0.404 6285 -
all-6603 -
obs--100 %

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