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- PDB-3wrf: The crystal structure of native HypBA1 from Bifidobacterium longu... -

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Basic information

Entry
Database: PDB / ID: 3wrf
TitleThe crystal structure of native HypBA1 from Bifidobacterium longum JCM 1217
ComponentsNon-reducing end beta-L-arabinofuranosidase
KeywordsHYDROLASE / glycoside hydrolase / arabinofuranose / b-L-arabinofuranosidase / one (a11/a6)-barrel fold / two b-jellyroll folds
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
Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHuang, C.H. / Zhu, Z. / Cheng, Y.S. / Chan, H.C. / Ko, T.P. / Chen, C.C. / Wang, I. / Ho, M.R. / Hsu, S.T. / Zeng, Y.F. ...Huang, C.H. / Zhu, Z. / Cheng, Y.S. / Chan, H.C. / Ko, T.P. / Chen, C.C. / Wang, I. / Ho, M.R. / Hsu, S.T. / Zeng, Y.F. / Huang, Y.N. / Liu, J.R. / Guo, R.T.
CitationJournal: J BIOPROCESS BIOTECH / Year: 2014
Title: Structure and Catalytic Mechanism of a Glycoside Hydrolase Family-127 beta-L-Arabinofuranosidase (HypBA1)
Authors: Huang, C.H. / Zhu, Z. / Cheng, Y.S. / Chan, H.C. / Ko, T.P. / Chen, C.C. / Wang, I. / Ho, M.R. / Hsu, S.T. / Zeng, Y.F. / Huang, Y.N. / Liu, J.R. / Guo, R.T.
History
DepositionFeb 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,8771
Polymers73,8771
Non-polymers00
Water5,026279
1
A: Non-reducing end beta-L-arabinofuranosidase

A: Non-reducing end beta-L-arabinofuranosidase


Theoretical massNumber of molelcules
Total (without water)147,7542
Polymers147,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5720 Å2
ΔGint-6 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.873, 75.873, 254.628
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-708-

HOH

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Components

#1: Protein Non-reducing end beta-L-arabinofuranosidase / Beta-L-arabinofuranosidase HypBA1


Mass: 73876.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: ATCC 15707 / Gene: hypBA1 / Plasmid: pET-29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.4M ammonium acetate, 18%(w/v) polyethylene glycol 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 41517 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 23.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4078 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2006 4.8 %RANDOM
Rwork0.215 38016 --
obs-40022 96.6 %-
Solvent computationBsol: 43.6267 Å2
Displacement parametersBiso max: 96.06 Å2 / Biso mean: 44.1445 Å2 / Biso min: 22.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.099 Å2-5.762 Å20 Å2
2---7.099 Å20 Å2
3---14.198 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 0 279 5297
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2541.5
X-RAY DIFFRACTIONc_scbond_it1.9662
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.25→2.33 Å /
RfactorNum. reflection
Rfree0.307 178
Rwork0.3 -

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