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- PDB-2y2w: Elucidation of the substrate specificity and protein structure of... -

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Basic information

Entry
Database: PDB / ID: 2y2w
TitleElucidation of the substrate specificity and protein structure of AbfB, a family 51 alpha-L-arabinofuranosidase from Bifidobacterium longum.
ComponentsARABINOFURANOSIDASE
KeywordsHYDROLASE / ARABINOXYLAN / GLYCOSIDE HYDROLASE FAMILY 51
Function / homology
Function and homology information


arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process / cytoplasm
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase / non-reducing end alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesBIFIDOBACTERIUM LONGUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLagaert, S. / Schoepe, J. / Delcour, J.A. / Lavigne, R. / Strelkov, S.V. / Courtin, C.M. / Mikkelsen, N.E. / Sandgren, M. / Volckaert, G.
CitationJournal: To be Published
Title: Elucidation of the Substrate Specificity and Protein Structure of Abfb, a Family 51 Alpha-L- Arabinofuranosidase from Bifidobacterium Longum.
Authors: Lagaert, S. / Schoepe, J. / Delcour, J.A. / Lavigne, R. / Strelkov, S.V. / Courtin, C.M. / Mikkelsen, N.E. / Sandgren, M. / Volckaert, G.
History
DepositionDec 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARABINOFURANOSIDASE
B: ARABINOFURANOSIDASE
C: ARABINOFURANOSIDASE
D: ARABINOFURANOSIDASE
E: ARABINOFURANOSIDASE
F: ARABINOFURANOSIDASE


Theoretical massNumber of molelcules
Total (without water)375,7286
Polymers375,7286
Non-polymers00
Water12,592699
1
A: ARABINOFURANOSIDASE
C: ARABINOFURANOSIDASE
D: ARABINOFURANOSIDASE


Theoretical massNumber of molelcules
Total (without water)187,8643
Polymers187,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-18.8 kcal/mol
Surface area53020 Å2
MethodPISA
2
B: ARABINOFURANOSIDASE
E: ARABINOFURANOSIDASE
F: ARABINOFURANOSIDASE


Theoretical massNumber of molelcules
Total (without water)187,8643
Polymers187,8643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-26 kcal/mol
Surface area54260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.469, 165.811, 184.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ARABINOFURANOSIDASE / ALPHA-L-ARABINOFURANOSIDASE


Mass: 62621.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BIFIDOBACTERIUM LONGUM (bacteria) / Strain: SP. LONGUM / Variant: BENEFLORA / Plasmid: PEXP5-CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL
References: UniProt: Q841V6, UniProt: Q8G554*PLUS, non-reducing end alpha-L-arabinofuranosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.44 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: ABFB CRYSTALS WERE OBTAINED BY MIXING 1 MICROLITER CONCENTRATED PROTEIN SOLUTION WITH 3 MICROLITER CRYSTALLIZATION SOLUTION CONTAINING 0.2 M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 20% W/V ...Details: ABFB CRYSTALS WERE OBTAINED BY MIXING 1 MICROLITER CONCENTRATED PROTEIN SOLUTION WITH 3 MICROLITER CRYSTALLIZATION SOLUTION CONTAINING 0.2 M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 20% W/V POLYETHYLENE GLYCOL 3350, USING THE VAPOR-DIFFUSION METHOD WITH HANGING OR SITTING DROPS AT 20-24 C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 109183 / % possible obs: 99.8 % / Observed criterion σ(I): 2.4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PZ3

1pz3


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.467 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.795 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26986 5776 5 %RANDOM
Rwork0.22014 ---
obs0.22263 109183 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.259 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---2.59 Å20 Å2
3---3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23544 0 0 699 24243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02124200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.921.93633033
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96553049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51724.3791128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.029153615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.89115131
X-RAY DIFFRACTIONr_chiral_restr0.0620.23583
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02118935
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2361.515265
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.439224446
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39638935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6944.58586
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 436 -
Rwork0.312 7899 -
obs--99.98 %

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