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- PDB-2rgm: Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase -

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Basic information

Entry
Database: PDB / ID: 2rgm
TitleRice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-alpha-barrels / Glycosidase
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 / Beta-glucosidase 7
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChuenchor, W. / Ketudat Cairns, J.R. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Chen, C.-J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Insights into Rice BGlu1 beta-Glucosidase Oligosaccharide Hydrolysis and Transglycosylation
Authors: Chuenchor, W. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Oonanant, W. / Bevan, D.R. / Esen, A. / Chen, C.J. / Opassiri, R. / Svasti, J. / Cairns, J.R.K.
History
DepositionOct 4, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.conn_type_id ..._chem_comp.type / _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 1.3Oct 25, 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.end_auth_comp_id
Revision 1.4Oct 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
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,65311
Polymers109,4572
Non-polymers1,1969
Water24,3561352
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3596
Polymers54,7281
Non-polymers6315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2945
Polymers54,7281
Non-polymers5664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.287, 101.286, 127.253
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: 6 / 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 / 2-F-Glucosylated Rice BGlu1 Beta-Glucosidase


Mass: 54728.465 Da / Num. of mol.: 2 / Fragment: Residues UNP 29-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Species: Oryza sativa / Strain: Orion / Gene: Os3bglu7 / Plasmid: pET32a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3)
References: UniProt: Q42975, UniProt: Q75I93*PLUS, 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, 1359 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1352 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 23% PEG MME 5000, 0.2M 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: 0.98008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. all: 157799 / Num. obs: 155944 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.5
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.29 / Num. unique all: 15186 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBG

1cbg


Resolution: 1.55→28.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.302 / SU ML: 0.048 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE WATERS LISTED IN REMARK 500 WERE CLEARLY EVIDENT IN THE DENSITY AND REFINED TO THESE POSITIONS, TYR 131 SEEMS TO HYDROGEN BOND WITH THE SAME OXYGEN (GLYCEROL O2) AS GLU176, WHICH IS THE ...Details: THE WATERS LISTED IN REMARK 500 WERE CLEARLY EVIDENT IN THE DENSITY AND REFINED TO THESE POSITIONS, TYR 131 SEEMS TO HYDROGEN BOND WITH THE SAME OXYGEN (GLYCEROL O2) AS GLU176, WHICH IS THE CATALYTIC ACID/BASE. GLU 386 IS COVALENTLY BOUND TO 2-FLUOROGLUCOSIDE AND THE SURROUNDING RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.19672 7487 5 %Copy R-free from 2RGL
Rwork0.17144 ---
all0.17272 157799 --
obs0.17272 141569 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 69 1352 9023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.93310730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91123.618398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.854151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5681544
X-RAY DIFFRACTIONr_chiral_restr0.1710.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.23968
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.21124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.281
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7641.54743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22227470
X-RAY DIFFRACTIONr_scbond_it2.04433677
X-RAY DIFFRACTIONr_scangle_it3.134.53260
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: 3812 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.055
loose thermal0.5910
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 526 -
Rwork0.25 10173 -
obs--97.56 %

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