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- PDB-6r4k: Structure of beta-glucosidase A from Paenibacillus polymyxa compl... -

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Basic information

Entry
Database: PDB / ID: 6r4k
TitleStructure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor
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-JSK / Beta-glucosidase A
Similarity search - Component
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 22, 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
Item: _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 A
B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0004
Polymers103,2172
Non-polymers7832
Water8,251458
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)416,00116
Polymers412,8708
Non-polymers3,1318
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3
MethodPISA
Unit cell
Length a, b, c (Å)146.725, 146.725, 140.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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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-JSK / (2~{S},3~{S},4~{R})-2-[[4-[4-[2-[2-(2-azanylidenehydrazinyl)ethoxy]ethoxy]phenyl]-1,2,3-triazol-1-yl]methyl]pyrrolidine-3,4-diol


Mass: 391.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.65 Å3/Da / Density % sol: 66.31 % / Description: Prismatic crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Bis-Tris propane, pH 7.5, and 5% n-Dodecyl 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: Jul 22, 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: 2.13→48.91 Å / Num. obs: 85545 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Net I/σ(I): 11.6
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4461 / CC1/2: 0.655 / Rpim(I) all: 0.299 / Rrim(I) all: 0.765 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimless7.0.057data scaling
MOLREP7.0.066phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E4I

1e4i


Resolution: 2.13→48.646 Å / Cross valid method: FREE R-VALUE / σ(F): 83 / Phase error: 28.92
RfactorNum. reflection% reflection
Rfree0.2413 4518 5.28 %
Rwork0.2159 --
obs0.2175 85512 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→48.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7294 0 56 458 7808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017574
X-RAY DIFFRACTIONf_angle_d1.210298
X-RAY DIFFRACTIONf_dihedral_angle_d7.7464316
X-RAY DIFFRACTIONf_chiral_restr0.0651046
X-RAY DIFFRACTIONf_plane_restr0.0091344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.16670.3262170.30373977X-RAY DIFFRACTION94
2.1667-2.20610.33192130.29434007X-RAY DIFFRACTION95
2.2061-2.24850.31572440.27623968X-RAY DIFFRACTION94
2.2485-2.29440.29272210.28544019X-RAY DIFFRACTION95
2.2944-2.34430.28272420.28123980X-RAY DIFFRACTION94
2.3443-2.39880.28562200.27493995X-RAY DIFFRACTION95
2.3988-2.45870.34092350.26894000X-RAY DIFFRACTION94
2.4587-2.52520.32552380.2654001X-RAY DIFFRACTION94
2.5252-2.59940.28532130.24954019X-RAY DIFFRACTION95
2.5994-2.68320.27222390.24364005X-RAY DIFFRACTION94
2.6832-2.7790.26472520.24754007X-RAY DIFFRACTION94
2.779-2.89020.27372090.24274014X-RAY DIFFRACTION95
2.8902-3.02160.26242260.23444054X-RAY DIFFRACTION95
3.0216-3.18060.25942130.22174075X-RAY DIFFRACTION95
3.1806-3.37960.23911820.20524107X-RAY DIFFRACTION96
3.3796-3.640.21622070.19554084X-RAY DIFFRACTION95
3.64-4.00520.18571910.17174116X-RAY DIFFRACTION95
4.0052-4.58240.17312360.1594079X-RAY DIFFRACTION94
4.5824-5.76440.18692120.17284167X-RAY DIFFRACTION95
5.7644-27.24840.22182370.1974341X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 11.8397 Å / Origin y: -39.7753 Å / Origin z: 45.1114 Å
111213212223313233
T0.1944 Å20.0047 Å20.252 Å2-0.1861 Å2-0.0153 Å2--0.4217 Å2
L0.3898 °20.0214 °20.1097 °2-0.3005 °2-0.0161 °2--0.0557 °2
S-0.0342 Å °0.0489 Å °0.3393 Å °-0.0438 Å °-0.0006 Å °-0.1071 Å °0.0197 Å °0.0416 Å °0.021 Å °
Refinement TLS groupSelection details: all

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