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- PDB-6wiu: Crystal structure of a beta-glucosidase from Exiguobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 6wiu
TitleCrystal structure of a beta-glucosidase from Exiguobacterium marinum
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesExiguobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.511 Å
AuthorsZanphorlin, L.M. / Morais, M.A.B. / Murakami, M.T.
CitationJournal: Biofuels, Bioprod Bioref / Year: 2020
Title: A rationally identified marine GH1 beta-glucosidase has distinguishing functional features for simultaneous saccharification and fermentation
Authors: de Sousa, A.S. / de Melo, R.R. / Miyamoto, R.Y. / Morais, M.A.B. / Andrade, L.P. / Milan, N. / de Avila, M.C. / de Souza, C.M. / Adao, R.C. / Scarpassa, J.A. / Vieira, P.S. / dos Santos, L.V. ...Authors: de Sousa, A.S. / de Melo, R.R. / Miyamoto, R.Y. / Morais, M.A.B. / Andrade, L.P. / Milan, N. / de Avila, M.C. / de Souza, C.M. / Adao, R.C. / Scarpassa, J.A. / Vieira, P.S. / dos Santos, L.V. / Ramos, C.H.I. / Murakami, M.T. / Zanphorlin, L.M.
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _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
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase
E: Beta-glucosidase
F: Beta-glucosidase
G: Beta-glucosidase
H: Beta-glucosidase
I: Beta-glucosidase
J: Beta-glucosidase
K: Beta-glucosidase
L: Beta-glucosidase
M: Beta-glucosidase
N: Beta-glucosidase
O: Beta-glucosidase
P: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)872,97216
Polymers872,97216
Non-polymers00
Water00
1
A: Beta-glucosidase
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)218,2434
Polymers218,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-26 kcal/mol
Surface area63390 Å2
MethodPISA
2
E: Beta-glucosidase
F: Beta-glucosidase
G: Beta-glucosidase
H: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)218,2434
Polymers218,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-25 kcal/mol
Surface area63650 Å2
MethodPISA
3
I: Beta-glucosidase
J: Beta-glucosidase
K: Beta-glucosidase
L: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)218,2434
Polymers218,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-28 kcal/mol
Surface area65810 Å2
MethodPISA
4
M: Beta-glucosidase
N: Beta-glucosidase
O: Beta-glucosidase
P: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)218,2434
Polymers218,2434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-27 kcal/mol
Surface area64520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.161, 171.897, 213.522
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-glucosidase


Mass: 54560.734 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sp. (strain ATCC BAA-1283 / AT1b) (bacteria)
Strain: ATCC BAA-1283 / AT1b / Gene: EAT1b_2183 / Production host: Escherichia coli (E. coli) / References: UniProt: C4L1S4*PLUS, beta-glucosidase

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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: 47.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 % (w/v) PEG 3350; 0.2 M sodium bromide; 0.1 M Bis tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 3.5→32.709 Å / Num. obs: 93391 / % possible obs: 99.7 % / Redundancy: 4.975 % / Biso Wilson estimate: 93.9 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.406 / Rrim(I) all: 0.454 / Χ2: 0.981 / Net I/σ(I): 3.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.715.1081.9940.827846415440153610.4382.22199.5
3.71-3.965.0791.4951.077380214542145310.4611.66799.9
3.96-4.284.8610.9961.556573213533135230.61.11799.9
4.28-4.684.5480.6632.275658112446124420.7490.752100
4.68-5.235.2510.5243.245925411291112840.850.58299.9
5.23-6.035.2230.4893.5352076998599700.8720.54399.8
6.03-7.364.9940.374.6142426850384960.9150.41399.9
7.36-10.284.5960.10513.4230345662266030.9930.11999.7
10.28-32.7094.9970.0526.8318993391138010.9970.05697.2

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Processing

Software
NameVersionClassification
PHENIX1.8.3refinement
XDSdata reduction
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DT5

5dt5


Resolution: 3.511→32.709 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.89
RfactorNum. reflection% reflection
Rfree0.2921 4491 4.81 %
Rwork0.2633 --
obs0.2647 93273 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 460.34 Å2 / Biso mean: 102.42 Å2 / Biso min: 38.01 Å2
Refinement stepCycle: final / Resolution: 3.511→32.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57949 0 0 0 57949
Num. residues----7059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00459714
X-RAY DIFFRACTIONf_angle_d1.14680909
X-RAY DIFFRACTIONf_chiral_restr0.058030
X-RAY DIFFRACTIONf_plane_restr0.00410571
X-RAY DIFFRACTIONf_dihedral_angle_d15.24121237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5113-3.55110.57941230.552248493
3.5511-3.59290.43141020.4483199696
3.5929-3.63660.39911580.36462993100
3.6366-3.68260.43731660.40172989100
3.6826-3.7310.38151640.36992950100
3.731-3.7820.33441470.31913050100
3.782-3.8360.32691560.32964100
3.836-3.89320.34551500.31463033100
3.8932-3.95390.34491490.32453032100
3.9539-4.01860.34391540.2992995100
4.0186-4.08780.37061510.29593027100
4.0878-4.1620.28721360.27872980100
4.162-4.24180.31881400.27283015100
4.2418-4.32820.30631330.27493031100
4.3282-4.42210.29381440.26593048100
4.4221-4.52470.28191450.25252971100
4.5247-4.63760.26261690.24383041100
4.6376-4.76260.27681440.24942998100
4.7626-4.90230.26121470.24783006100
4.9023-5.060.29281390.24653083100
5.06-5.24010.28771530.2362964100
5.2401-5.4490.26991640.24243031100
5.449-5.69580.26471550.24813005100
5.6958-5.99440.30131620.24392987100
5.9944-6.36730.26191360.25263056100
6.3673-6.85480.29421680.25243003100
6.8548-7.5370.28691650.24013043100
7.537-8.61020.24061450.22113027100
8.6102-10.7830.21091720.19173025100

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