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- PDB-7bbs: Structure of Bg10: an alcohol-tolerant and glucose-stimulated B-g... -

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Basic information

Entry
Database: PDB / ID: 7bbs
TitleStructure of Bg10: an alcohol-tolerant and glucose-stimulated B-glucosidase
ComponentsBeta-glucosidase Bg10
KeywordsHYDROLASE / Glucose-stimulated / GH1 family / metagenomics
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
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
Beta-glucosidase Bg10
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaldaner Pereira, P.A. / Gomes-Pepe, E.S. / Silva, S.T.N. / Matias, P.M. / Lemos, E.G.M.
Funding support Brazil, Portugal, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/10981-3 Brazil
Foundation for Science and Technology (FCT)LISBOA-01-0145-FEDER-007660 Portugal
CitationJournal: TO BE PUBLISHED
Title: Structure of Bg10: an alcohol-tolerant and glucose-stimulated beta-glucosidase
Authors: Maldaner Pereira, P.A. / Gomes-Pepe, E.S. / Silva, S.T.N. / Matias, P.M. / Lemos, E.G.M.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase Bg10
B: Beta-glucosidase Bg10


Theoretical massNumber of molelcules
Total (without water)108,4662
Polymers108,4662
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-3 kcal/mol
Surface area31330 Å2
Unit cell
Length a, b, c (Å)92.432, 138.485, 114.841
Angle α, β, γ (deg.)90.000, 102.466, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 17 through 323 or resid 341 through 484))
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERHISA1 - 307
d_12ens_1SERPROA309 - 452
d_21ens_1SERPROB1 - 451

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Components

#1: Protein Beta-glucosidase Bg10


Mass: 54233.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L3HS62, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.32 Å3/Da / Density % sol: 62.9 % / Description: diamond-shaped plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12% (v/v) PEG 3550, 250 mM potassium citrate, 4% (v/v) 1,5-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→112.13 Å / Num. obs: 33702 / % possible obs: 54.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.94 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.124 / Rrim(I) all: 0.23 / Net I/σ(I): 5.6
Reflection shellResolution: 2.3→2.604 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1686 / CC1/2: 0.584 / Rpim(I) all: 0.486 / Rrim(I) all: 0.809 / % possible all: 8.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNX

1gnx


Resolution: 2.3→112.13 Å / SU ML: 0.336 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 1716 5.09 %Random selection
Rwork0.228 31972 --
obs0.2301 33688 53.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→112.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 0 21 7117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00187311
X-RAY DIFFRACTIONf_angle_d0.52469999
X-RAY DIFFRACTIONf_chiral_restr0.03961057
X-RAY DIFFRACTIONf_plane_restr0.00361316
X-RAY DIFFRACTIONf_dihedral_angle_d10.95672579
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.42353283856 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.570340.415638X-RAY DIFFRACTION0.83
2.37-2.440.2653160.3074248X-RAY DIFFRACTION5.14
2.44-2.530.3518330.2869583X-RAY DIFFRACTION11.92
2.53-2.630.3751660.29631021X-RAY DIFFRACTION20.99
2.63-2.750.2936870.29181652X-RAY DIFFRACTION33.6
2.75-2.90.34241010.29212499X-RAY DIFFRACTION49.8
2.9-3.080.33021790.27813178X-RAY DIFFRACTION64.22
3.08-3.320.32092220.26323788X-RAY DIFFRACTION77.25
3.32-3.650.30122510.24384306X-RAY DIFFRACTION87.55
3.65-4.180.24362430.21364775X-RAY DIFFRACTION95.34
4.18-5.260.2422590.19534881X-RAY DIFFRACTION98.68
5.26-112.130.21492550.19435003X-RAY DIFFRACTION98.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7331777963780.1663030139330.0741011118991.00618976639-0.005748716874820.520359945127-0.08849710603620.01326728122170.000821768319397-0.0347893825970.0880285354547-0.1181657739510.009705030919790.06597340194560.0002730003728090.155619276271-0.04034338966140.0008782238603980.1115956963830.002970692913260.13390453156529.1644759133-25.188442488426.3396766891
20.6407178829760.0401475259112-0.2985272220331.066650755140.0279128762470.567322187908-0.0386976332582-0.054961324348-0.04178468373680.04782560437020.05843159695460.155572881244-0.0757414411247-0.0615377201793-0.01020777911960.122235575252-0.0350965210972-0.01794040655330.104520361688-0.000264027840140.081232466516838.389974108315.180994782525.3814896106
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 17 - 484

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain 'B' and resid 17 through 484)BB1 - 451
22(chain 'A' and resid 17 through 484)AA1 - 452

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