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- PDB-3wba: Rice Os3BGlu6 E178Q with Covalent Glucosyl Moiety from p-nitrophe... -

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Basic information

Entry
Database: PDB / ID: 3wba
TitleRice Os3BGlu6 E178Q with Covalent Glucosyl Moiety from p-nitrophenyl glucopyranoside.
ComponentsBeta-glucosidase 6
KeywordsHYDROLASE / TIM BARREL / Beta-glucosidase / Covalently bound to Glucose / Secreted
Function / homology
Function and homology information


cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / glucan endo-1,3-beta-D-glucosidase activity / hydrolase activity, acting on glycosyl bonds / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
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
alpha-D-glucopyranose / Beta-glucosidase 6
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.9 Å
AuthorsSansenya, S. / Hua, Y. / Cairns, J.R.K.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice beta-d-glucosidase
Authors: Hua, Y. / Sansenya, S. / Saetang, C. / Wakuta, S. / Cairns, J.R.K.
History
DepositionMay 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0147
Polymers55,3731
Non-polymers6416
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.986, 91.127, 111.221
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 Beta-glucosidase 6 / Os3bglu6


Mass: 55373.000 Da / Num. of mol.: 1 / Fragment: UNP residues 38-521 / Mutation: E178Q
Source method: isolated from a genetically manipulated source
Details: Amplified from seedlings & cloned into pENTR/TEV/D-TOPO, then recombined to
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Strain: Yukihikari (japonica) / Gene: BGLU6, LOC_Os03g11420, Os03g0212800 / Plasmid: pET32a(+)/DEST / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: Q8L7J2, beta-glucosidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% PEG5000MME, 0.1M Bis/Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2011 / Details: toroidal focusing mirror
RadiationMonochromator: LN2-cooled, fixed-exit double crystal monochromator, Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25.67 Å / Num. all: 46100 / Num. obs: 45797 / % possible obs: 97.84 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: PDB ENTRY 3GNO

3gno


Resolution: 1.9→25.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17872 2307 5.1 %RANDOM
Rwork0.14617 ---
obs0.14781 43044 97.84 %-
all-43994 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.847 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 41 534 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224079
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9335540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22423.529204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84815633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0451525
X-RAY DIFFRACTIONr_chiral_restr0.0930.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213188
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_it0.6951.52423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3123896
X-RAY DIFFRACTIONr_scbond_it1.97131656
X-RAY DIFFRACTIONr_scangle_it3.144.51644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 149 -
Rwork0.178 2762 -
obs--87.23 %

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