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- PDB-4qll: Crystal structure of rice BGlu1 E176Q/Y341A/Q187A mutant complexe... -

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Basic information

Entry
Database: PDB / ID: 4qll
TitleCrystal structure of rice BGlu1 E176Q/Y341A/Q187A mutant complexed with cellotetraose
ComponentsBeta-glucosidase 7
KeywordsHYDROLASE / BETA-ALPHA-BARRELS / OLIGOSACCHARIDE BINDING / 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 / scopolin beta-glucosidase activity / beta-glucosidase 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 / scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / beta-galactosidase 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
beta-cellotetraose / Beta-glucosidase 7
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 1.85 Å
AuthorsPengthaisong, S. / Ketudat Cairns, J.R.
CitationJournal: Protein Sci. / Year: 2014
Title: Effects of active site cleft residues on oligosaccharide binding, hydrolysis, and glycosynthase activities of rice BGlu1 and its mutants
Authors: Pengthaisong, S. / Ketudat Cairns, J.R.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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

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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)111,80410
Polymers109,1572
Non-polymers2,6488
Water15,115839
1
A: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2686
Polymers54,5781
Non-polymers1,6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5364
Polymers54,5781
Non-polymers9583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.581, 101.257, 127.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999981, 0.002688, 0.005521), (0.002719, 0.99998, 0.005773), (-0.005506, 0.005788, -0.999968)0.16064, -0.07339, 24.83972

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Beta-glucosidase 7 / / Os3bglu7


Mass: 54578.340 Da / Num. of mol.: 2 / Mutation: E176Q/Y341A/Q187A
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
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 844 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 47.7 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG MME 5000, 0.18M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: Dec 13, 2012
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: 85615 / % possible obs: 97.5 % / Redundancy: 7.5 % / Rsym value: 0.077 / Net I/σ(I): 25.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 8338 / Rsym value: 0.416 / % possible all: 96.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
Cootmodel building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Rigid body refinement
Starting model: 3F5I

3f5i
PDB Unreleased entry


Resolution: 1.85→27.93 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.455 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18517 4250 5 %RANDOM
Rwork0.16104 ---
obs0.16223 81095 96.85 %-
all-85615 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.547 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-0 Å2
2--1.23 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 170 839 8605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198004
X-RAY DIFFRACTIONr_bond_other_d0.0060.027251
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.94710899
X-RAY DIFFRACTIONr_angle_other_deg1.015316637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20123.668398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7721544
X-RAY DIFFRACTIONr_chiral_restr0.1220.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022056
X-RAY DIFFRACTIONr_mcbond_it0.7071.5713774
X-RAY DIFFRACTIONr_mcbond_other0.7061.5713773
X-RAY DIFFRACTIONr_mcangle_it1.1242.3514714
X-RAY DIFFRACTIONr_mcangle_other1.1242.3524715
X-RAY DIFFRACTIONr_scbond_it1.2221.7744230
X-RAY DIFFRACTIONr_scbond_other1.2221.7744230
X-RAY DIFFRACTIONr_scangle_other1.9562.6056186
X-RAY DIFFRACTIONr_long_range_B_refined4.27814.12310029
X-RAY DIFFRACTIONr_long_range_B_other3.93113.5619667
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 284 -
Rwork0.196 5544 -
obs-8338 91.43 %

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