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- PDB-7exu: GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed wi... -

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Basic information

Entry
Database: PDB / ID: 7exu
TitleGH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside
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-07Y / Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsMaruyama, S. / Arakawa, T. / Yamada, C. / Fujita, K. / 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: Glycobiology / Year: 2022
Title: Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase.
Authors: Maruyama, S. / Sawano, K. / Amaki, S. / Suzuki, T. / Narita, S. / Kimura, K. / Arakawa, T. / Yamada, C. / Ito, Y. / Dohmae, N. / Fujita, K. / Ishiwata, A. / Fushinobu, S.
#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
DepositionMay 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Feb 21, 2024Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.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)74,7943
Polymers74,4571
Non-polymers3372
Water45025
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)149,5876
Polymers148,9142
Non-polymers6734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5650 Å2
ΔGint-6 kcal/mol
Surface area43260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.182, 78.182, 253.502
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: 74456.922 Da / Num. of mol.: 1 / Mutation: E322Q
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: pET23 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
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: Sugar ChemComp-07Y / (2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol


Type: saccharide / Mass: 271.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.7 M sodium citrate, 0.1 M MES-NaOH (pH 6.5), 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.31 Å / Num. obs: 41037 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 49.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.036 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.1 % / Rmerge(I) obs: 3.663 / Mean I/σ(I) obs: 1 / Num. unique obs: 3910 / CC1/2: 0.728 / Rpim(I) all: 1.144 / % possible all: 100

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Processing

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

3wkx


Resolution: 2.3→46.31 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.275 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 2114 5.2 %RANDOM
Rwork0.2516 ---
obs0.2536 38851 99.97 %-
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 max: 149.13 Å2 / Biso mean: 68.703 Å2 / Biso min: 44.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.53 Å20 Å2
2--1.05 Å2-0 Å2
3----3.41 Å2
Refinement stepCycle: final / Resolution: 2.3→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 20 25 5143
Biso mean--80.5 59.75 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135238
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174761
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6477123
X-RAY DIFFRACTIONr_angle_other_deg1.2551.58510942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48122.375299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80115813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4621536
X-RAY DIFFRACTIONr_chiral_restr0.0580.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021243
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 149 -
Rwork0.332 2790 -
all-2939 -
obs--100 %

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