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- PDB-6m5a: Crystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bi... -

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Basic information

Entry
Database: PDB / ID: 6m5a
TitleCrystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bifidobacterium longum
ComponentsBeta-L-arabinobiosidase
KeywordsHYDROLASE / (alpha/alpha)6 barrel / glycoside hydrolase family 121
Function / homology
Function and homology information


(Ara-f)3-Hyp beta-L-arabinobiosidase / hydrolase activity, acting on glycosyl bonds / polysaccharide catabolic process / membrane => GO:0016020 / carbohydrate metabolic process
Similarity search - Function
Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta-L-arabinobiosidase / Beta-L-arabinobiosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsSaito, K. / Arakawa, T. / Yamada, C. / Fujita, K. / Fushinobu, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24380053 Japan
Japan Society for the Promotion of Science (JSPS)22780094 Japan
Japan Society for the Promotion of Science (JSPS)26660083 Japan
Japan Society for the Promotion of Science (JSPS)15H02443 Japan
Citation
Journal: Plos One / Year: 2020
Title: Crystal structure of beta-L-arabinobiosidase belonging to glycoside hydrolase family 121.
Authors: Saito, K. / Viborg, A.H. / Sakamoto, S. / Arakawa, T. / Yamada, C. / Fujita, K. / Fushinobu, S.
#1: Journal: J. Biol. Chem. / Year: 2011
Title: Molecular cloning and characterization of a beta-L-Arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family.
Authors: Fujita, K. / Sakamoto, S. / Ono, Y. / Wakao, M. / Suda, Y. / Kitahara, K. / Suganuma, T.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-L-arabinobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,32927
Polymers96,9451
Non-polymers2,38526
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint44 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.526, 88.616, 127.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-L-arabinobiosidase


Mass: 96944.609 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: DWV93_04865 / Plasmid: pET-23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: A0A413AH52, UniProt: E8MGH9*PLUS

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Non-polymers , 6 types, 575 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.43 % / Description: Pillar
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 17% (w/v) PEG1000 and 0.1 M Tris-HCl (pH 6.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 4, 2016
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→44.35 Å / Num. obs: 79741 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.018 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.051 / Χ2: 0.86 / Net I/σ(I): 9.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7 % / Rmerge(I) obs: 1.405 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4473 / CC1/2: 0.634 / Rpim(I) all: 0.571 / Χ2: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
Aimlessphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→44.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.065 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.109
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 3934 4.9 %RANDOM
Rwork0.158 ---
obs0.1594 75729 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.76 Å2 / Biso mean: 27.5 Å2 / Biso min: 17.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.85→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 152 549 7337
Biso mean--52.71 39.67 -
Num. residues----844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175996
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.6469358
X-RAY DIFFRACTIONr_angle_other_deg1.4981.57813978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35324.709378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.078151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9491522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021419
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 258 -
Rwork0.27 5530 -
all-5788 -
obs--100 %

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