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- PDB-6qwi: Structure of beta-glucosidase A from Paenibacillus polymyxa compl... -

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Basic information

Entry
Database: PDB / ID: 6qwi
TitleStructure of beta-glucosidase A from Paenibacillus polymyxa complexed with multivalent inhibitors.
ComponentsBeta-glucosidase A
KeywordsHYDROLASE / BETA-GLUCOSIDASE / GLYCOSIDASE / CARBOHYDRATE / CARBOHYDRATE METABOLISM / POLISACCHARIDE DEGRADATION / COMPLEX / INHIBITOR
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-JJW / Beta-glucosidase A
Similarity search - Component
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsJimenez-Ortega, E. / Sanz-Aparicio, J.
CitationJournal: Bioorg.Chem. / Year: 2019
Title: Structural basis of the inhibition of GH1 beta-glucosidases by multivalent pyrrolidine iminosugars.
Authors: Martinez-Bailen, M. / Jimenez-Ortega, E. / Carmona, A.T. / Robina, I. / Sanz-Aparicio, J. / Talens-Perales, D. / Polaina, J. / Matassini, C. / Cardona, F. / Moreno-Vargas, A.J.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _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 A
B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9144
Polymers103,2172
Non-polymers6972
Water2,648147
1
A: Beta-glucosidase A
B: Beta-glucosidase A
hetero molecules

A: Beta-glucosidase A
B: Beta-glucosidase A
hetero molecules

A: Beta-glucosidase A
B: Beta-glucosidase A
hetero molecules

A: Beta-glucosidase A
B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,65716
Polymers412,8708
Non-polymers2,7878
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)146.096, 146.096, 140.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-705-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 448 / Label seq-ID: 1 - 448

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

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Components

#1: Protein Beta-glucosidase A / BGA / Amygdalase / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase


Mass: 51608.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Gene: bglA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / References: UniProt: P22073, beta-glucosidase
#2: Chemical ChemComp-JJW / (2~{S},3~{S},4~{R})-2-[[4-[4-(2-ethoxyethoxy)phenyl]-1,2,3-triazol-1-yl]methyl]pyrrolidine-3,4-diol


Mass: 348.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 3.64 Å3/Da / Density % sol: 66.23 % / Description: Prismatic crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD) and 0.1 M BisTris propane, pH 7.5 and 0.56 mM 6-Cyclohexylhexyl beta-D-maltoside. Cryoprotectant mother liquor ...Details: 13% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD) and 0.1 M BisTris propane, pH 7.5 and 0.56 mM 6-Cyclohexylhexyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 14, 2018 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.85→48.7 Å / Num. obs: 27295 / % possible obs: 76.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 45.005 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.052 / Rrim(I) all: 0.151 / Net I/σ(I): 10.3
Reflection shellResolution: 2.85→3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4060 / CC1/2: 0.804 / Rpim(I) all: 0.252 / Rrim(I) all: 0.737 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless7.0.057data scaling
MOLREP7.0.057phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E4I

1e4i


Resolution: 2.85→48.52 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.537 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23128 1405 5.2 %RANDOM
Rwork0.18056 ---
obs0.18315 25865 75.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.85→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7294 0 50 150 7494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137568
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176568
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.64510292
X-RAY DIFFRACTIONr_angle_other_deg1.2591.5815190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08722.227458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.423151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.541550
X-RAY DIFFRACTIONr_chiral_restr0.0580.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021780
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_it2.4864.6163582
X-RAY DIFFRACTIONr_mcbond_other2.4724.6163581
X-RAY DIFFRACTIONr_mcangle_it3.9116.9234473
X-RAY DIFFRACTIONr_mcangle_other3.9116.9244474
X-RAY DIFFRACTIONr_scbond_it2.6224.8333986
X-RAY DIFFRACTIONr_scbond_other2.6224.8333987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2927.1525819
X-RAY DIFFRACTIONr_long_range_B_refined6.56652.8838712
X-RAY DIFFRACTIONr_long_range_B_other6.56252.8898708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15452 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 99 -
Rwork0.293 1951 -
obs--78.33 %

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