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- PDB-3aht: Crystal structure of rice BGlu1 E176Q mutant in complex with lami... -

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Basic information

Entry
Database: PDB / ID: 3aht
TitleCrystal structure of rice BGlu1 E176Q mutant in complex with laminaribiose
ComponentsBeta-glucosidase 7
KeywordsHYDROLASE / BETA-ALPHA-BARRELS / GLYCOSIDE HYDROLASE / OLIGOSACCHARIDE
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-laminaribiose / Beta-glucosidase 7
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChuenchor, W. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Svasti, J. / Ketudat Cairns, J.R.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: The structural basis of oligosaccharide binding by rice BGlu1 beta-glucosidase
Authors: Chuenchor, W. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Svasti, J. / Ketudat Cairns, J.R.
History
DepositionApr 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _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 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

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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)110,7889
Polymers109,4552
Non-polymers1,3337
Water1,27971
1
A: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4265
Polymers54,7271
Non-polymers6994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3614
Polymers54,7271
Non-polymers6343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.704, 101.476, 128.291
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: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 6 - 476 / Label seq-ID: 11 - 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: 54727.480 Da / Num. of mol.: 2 / Mutation: E176Q
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-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 76 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.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCOORDINATE RESIDUE NUMBER 24 (UNP RESIDUE NUMBER 52) VAL IS A SEQUENCE CONFLICT IN REFRENCE 1 OF ...COORDINATE RESIDUE NUMBER 24 (UNP RESIDUE NUMBER 52) VAL IS A SEQUENCE CONFLICT IN REFRENCE 1 OF DATABASE UNIPROTKB/SWISS-PROT Q75I93 (BGL07_ORYSJ).

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 22% PEG MME 5000, 0.18M AMMONIUM, SULFATE, 0.1M MES, SOAKED WITH 0.010 M LAMINARIBIOSE, 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: Jul 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25.7 Å / Num. all: 26210 / Num. obs: 25956 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 16.1
Reflection shellResolution: 2.8→2.94 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2544 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.0 (rigid body refinement for isomorphous crystal)refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.0 (rigid body refinement for isomorphous crystal)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3F4V

3f4v


Resolution: 2.8→25.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.28 / SU ML: 0.264 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The crystal has high occupancy laminaribiose in 3AHT, but low occupancy in 3F5L; 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24836 1273 4.9 %RANDOM
Rwork0.20525 ---
all0.238 26210 --
obs0.20737 24681 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.228 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0 Å20 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.333 Å
Refinement stepCycle: LAST / Resolution: 2.8→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 81 71 7754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227916
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.93310766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.895940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03823.65400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9621544
X-RAY DIFFRACTIONr_chiral_restr0.1060.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216204
X-RAY DIFFRACTIONr_mcbond_it0.2841.54674
X-RAY DIFFRACTIONr_mcangle_it0.58427482
X-RAY DIFFRACTIONr_scbond_it0.91733242
X-RAY DIFFRACTIONr_scangle_it1.584.53284
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3801 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.020.05
tight thermal0.130.5
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 91 -
Rwork0.263 1578 -
obs--88.73 %

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