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- PDB-3aiq: Crystal structure of beta-glucosidase in wheat complexed with an ... -

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Basic information

Entry
Database: PDB / ID: 3aiq
TitleCrystal structure of beta-glucosidase in wheat complexed with an aglycone DIMBOA
ComponentsBeta-glucosidase
KeywordsHYDROLASE / TIM barrel / glycosidases
Function / homology
Function and homology information


DIMBOA glucoside beta-D-glucosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / beta-glucosidase / beta-glucosidase activity / chloroplast / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-HBO / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSue, M. / Nakamura, C. / Miyamoto, T. / Yajima, S.
CitationJournal: Plant Sci. / Year: 2011
Title: Active-site architecture of benzoxazinone-glucoside beta-D-glucosidases in Triticeae
Authors: Sue, M. / Nakamura, C. / Miyamoto, T. / Yajima, S.
History
DepositionMay 18, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3782
Polymers64,1671
Non-polymers2111
Water12,502694
1
A: Beta-glucosidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)386,26612
Polymers384,9996
Non-polymers1,2676
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area16070 Å2
ΔGint-54 kcal/mol
Surface area97540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.962, 193.962, 193.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Beta-glucosidase


Mass: 64166.574 Da / Num. of mol.: 1 / Fragment: residues in UNP 50-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: Taglu1b / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3) Ril / References: UniProt: Q1XH05, beta-glucosidase
#2: Chemical ChemComp-HBO / 2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE


Mass: 211.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 4.74 Å3/Da / Density % sol: 74.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10mM HEPES, 1M LiSO4, 150mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2006
RadiationMonochromator: triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 100930 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 42.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DGA

2dga


Resolution: 1.9→43.4 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 --RNADOM
Rwork0.195 ---
obs-92559 99.7 %-
Displacement parametersBiso mean: 21.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 15 694 4678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.344
X-RAY DIFFRACTIONr_chiral_restr0.104
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_nbd_refined0.237
X-RAY DIFFRACTIONr_nbtor_refined0.328
X-RAY DIFFRACTIONc_mcbond_it1.134
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.258 335 -
Rwork0.248 --
obs-4859 99.9 %

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