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- PDB-3ahv: Semi-active E176Q mutant of rice bglu1 covalent complex with 2-de... -

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Basic information

Entry
Database: PDB / ID: 3ahv
TitleSemi-active E176Q mutant of rice bglu1 covalent complex with 2-deoxy-2-fluoroglucoside
ComponentsBeta-glucosidase 7
KeywordsHYDROLASE / BETA-ALPHA-BARRELS / GLYCOSIDE HYDROLASE / COVALENT INTERMEDIATE
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
2-deoxy-2-fluoro-alpha-D-glucopyranose / Beta-glucosidase 7
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 30, 2010Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 2, 2010ID: 3F5I
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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 1.4Oct 23, 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)110,83613
Polymers109,4552
Non-polymers1,38111
Water11,926662
1
A: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4517
Polymers54,7271
Non-polymers7236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3856
Polymers54,7271
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.226, 100.387, 127.407
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: 54727.480 Da / Num. of mol.: 2 / Mutation: E176Q
Source method: isolated from a genetically manipulated source
Details: Produced as thioredoxin-His6-tag fusion protein, then removed from tag with enterokinase.
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: Sugar ChemComp-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 671 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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 22% 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: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. all: 80389 / Num. obs: 79635 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 6.1 / Num. unique all: 7908 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBG

1cbg


Resolution: 1.89→27.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.373 / SU ML: 0.074 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21339 3948 4.9 %COPIED FROM 2RGL AND RANDOMLY EXTENDED
Rwork0.18944 ---
obs0.19062 76370 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--1.89 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.137 Å0.162 Å
Luzzati sigma a-0.18 Å
Refinement stepCycle: LAST / Resolution: 1.89→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7618 0 81 662 8361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227926
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.93110768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31823.682402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.818151206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7791544
X-RAY DIFFRACTIONr_chiral_restr0.1640.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216220
X-RAY DIFFRACTIONr_mcbond_it0.7121.54684
X-RAY DIFFRACTIONr_mcangle_it1.29527498
X-RAY DIFFRACTIONr_scbond_it2.133242
X-RAY DIFFRACTIONr_scangle_it3.3224.53270
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3809 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.030.05
TIGHT THERMAL0.170.5
LS refinement shellResolution: 1.891→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 265 -
Rwork0.212 4939 -
obs--87.2 %

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