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- PDB-3scs: Crystal Structure of Rice BGlu1 E386S Mutant Complexed with alpha... -

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Basic information

Entry
Database: PDB / ID: 3scs
TitleCrystal Structure of Rice BGlu1 E386S Mutant Complexed with alpha-Glucosyl Fluoride
ComponentsBeta-glucosidase 7
KeywordsHYDROLASE / BETA-ALPHA-BARRELS / GLYCOSYNTHASE / OLIGOSACCHARIDE SYNTHESIS / TRANSGLUCOSYLATION
Function / homology
Function and homology information


amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / beta-glucosidase / beta-galactosidase activity ...amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process / protein homodimerization activity / extracellular region
Similarity search - Function
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-glucopyranosyl fluoride / Beta-glucosidase 7
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPengthaisong, S. / Withers, S.G. / Kuaprasert, B. / Ketudat Cairns, J.R.
CitationJournal: to be published
Title: Structural investigation of the basis for cellooligosaccharide synthesis by rice BGlu1 glycosynthases
Authors: Pengthaisong, S. / Withers, S.G. / Kuaprasert, B. / Ketudat Cairns, J.R.
History
DepositionJun 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase 7
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,56911
Polymers109,3732
Non-polymers1,1969
Water15,673870
1
A: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3176
Polymers54,6861
Non-polymers6315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2525
Polymers54,6861
Non-polymers5664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.128, 100.860, 127.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 5 - 476 / Label seq-ID: 10 - 481

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Beta-glucosidase 7 / Os3bglu7


Mass: 54686.430 Da / Num. of mol.: 2 / Mutation: E386S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Strain: ORION
Gene: BGLU1, BGLU7, LOC_Os03g49600, Os03g0703000, os3bglu7, OSJNBa0004L11.16
Plasmid: pET32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: Q75I93, beta-glucosidase
#6: Sugar ChemComp-GLF / alpha-D-glucopyranosyl fluoride / 1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE / alpha-D-glucosyl fluoride / D-glucosyl fluoride / glucosyl fluoride


Type: D-saccharide / Mass: 182.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp1fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 877 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONFLICT IS IN GENBANK DATABASE AAA84906.

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG MME 5000, 0.22M ammonium sulfate, 0.1M MES, 0.010M alpha-glucosyl fluoride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 87779 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.122 / Net I/σ(I): 16.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 8689 / Rsym value: 0.437 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0110phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGL

2rgl


Resolution: 1.85→25.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.366 / SU ML: 0.074 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20453 4328 4.9 %RANDOM
Rwork0.17382 ---
obs0.17533 83372 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7612 0 71 870 8553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.93110754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03823.65400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.139151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7131544
X-RAY DIFFRACTIONr_chiral_restr0.1560.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216212
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_it0.5861.54684
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10827498
X-RAY DIFFRACTIONr_scbond_it1.91433228
X-RAY DIFFRACTIONr_scangle_it3.1194.53256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3806 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.120.5
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 310 -
Rwork0.21 6067 -
obs-6067 99.42 %

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