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- PDB-3wrg: The complex structure of HypBA1 with L-arabinose -

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Basic information

Entry
Database: PDB / ID: 3wrg
TitleThe complex structure of HypBA1 with L-arabinose
ComponentsNon-reducing end beta-L-arabinofuranosidase
KeywordsHYDROLASE / glycoside hydrolase / arabinofuranose / beta-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
: / : / : / Beta-L-arabinofuranosidase, GH127 middle domain / Glycoside hydrolase family 127 C-terminal domain / Beta-L-arabinofuranosidase, GH127 / Beta-L-arabinofuranosidase, GH127 catalytic domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
beta-L-arabinofuranose / Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,3893
Polymers73,1741
Non-polymers2162
Water5,549308
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)146,7786
Polymers146,3472
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5560 Å2
ΔGint-1 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.586, 77.586, 254.176
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 73173.508 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: Sugar ChemComp-FUB / beta-L-arabinofuranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArafbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinofuranoseCOMMON NAMEGMML 1.0
b-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
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: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→25 Å / Num. obs: 43124 / % possible obs: 97.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.2
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4226 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2027 4.6 %RANDOM
Rwork0.204 38497 --
obs-40524 91.4 %-
Solvent computationBsol: 41.4304 Å2
Displacement parametersBiso max: 91.8 Å2 / Biso mean: 52.4154 Å2 / Biso min: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1--8.257 Å2-6.269 Å20 Å2
2---8.257 Å20 Å2
3---16.514 Å2
Refinement stepCycle: LAST / Resolution: 2.23→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 11 308 5471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3221.5
X-RAY DIFFRACTIONc_scbond_it2.0072
X-RAY DIFFRACTIONc_mcangle_it2.0752
X-RAY DIFFRACTIONc_scangle_it2.8062.5
LS refinement shellResolution: 2.23→2.31 Å /
RfactorNum. reflection
Rfree0.328 171
Rwork0.287 -

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