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- PDB-5wka: Crystal structure of a GH1 beta-glucosidase retrieved from microb... -

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Basic information

Entry
Database: PDB / ID: 5wka
TitleCrystal structure of a GH1 beta-glucosidase retrieved from microbial metagenome of Poraque Amazon lake
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Beta-glucosidase / GH1-family / metagenome
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMorais, M.A.B. / Toyama, D. / Ramos, F.C. / Zanphorlin, L.M. / Tonoli, C.C.C. / Miranda, F.P. / Ruller, R. / Henrique-Silva, F. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: A novel beta-glucosidase isolated from the microbial metagenome of Lake Poraque (Amazon, Brazil).
Authors: Toyama, D. / de Morais, M.A.B. / Ramos, F.C. / Zanphorlin, L.M. / Tonoli, C.C.C. / Balula, A.F. / de Miranda, F.P. / Almeida, V.M. / Marana, S.R. / Ruller, R. / Murakami, M.T. / Henrique-Silva, F.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,88814
Polymers211,9114
Non-polymers97710
Water18010
1
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3526
Polymers105,9552
Non-polymers3964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-4 kcal/mol
Surface area31570 Å2
MethodPISA
2
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5368
Polymers105,9552
Non-polymers5816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-8 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.471, 56.652, 209.546
Angle α, β, γ (deg.)90.000, 96.660, 90.000
Int Tables number5
Space group name H-MC121
Detailshomodimer by SAXS

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Components

#1: Protein
Beta-glucosidase /


Mass: 52977.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, PEG 6000 20% (w/v) and 0.2 M sodium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.75→46.463 Å / Num. obs: 49452 / % possible obs: 88.17 % / Redundancy: 3 % / Biso Wilson estimate: 57 Å2 / Net I/σ(I): 6
Reflection shell
Lowest resolution (Å)Diffraction-ID
1
1
1
1
46.4631

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNX

1gnx


Resolution: 2.75→46.463 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 32.55
RfactorNum. reflection% reflection
Rfree0.2703 4044 4.67 %
Rwork0.2321 --
obs0.2339 49452 88.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.83 Å2 / Biso mean: 56.983 Å2 / Biso min: 36.9 Å2
Refinement stepCycle: final / Resolution: 2.75→46.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14742 0 64 10 14816
Biso mean--71.84 52.53 -
Num. residues----1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215229
X-RAY DIFFRACTIONf_angle_d0.67220773
X-RAY DIFFRACTIONf_chiral_restr0.0262167
X-RAY DIFFRACTIONf_plane_restr0.0042728
X-RAY DIFFRACTIONf_dihedral_angle_d12.1715347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7502-2.78250.4487910.39932148223967
2.7825-2.81650.38011220.37872365248771
2.8165-2.85210.36771250.36132488261380
2.8521-2.88960.36731190.36212754287383
2.8896-2.92920.35921420.36282640278282
2.9292-2.97110.35581190.35792706282583
2.9711-3.01540.35991500.36722693284384
3.0154-3.06250.38231380.3522678281685
3.0625-3.11270.36331340.34632852298686
3.1127-3.16640.39941240.34372765288987
3.1664-3.22390.42861520.3172929308190
3.2239-3.28590.3321440.2862918306291
3.2859-3.3530.32121310.27032948307990
3.353-3.42590.34151150.27012879299491
3.4259-3.50550.29251440.263064320892
3.5055-3.59320.3071350.25642875301090
3.5932-3.69030.30111390.24242934307391
3.6903-3.79880.31151250.22433021314690
3.7988-3.92140.23351440.23412884302892
3.9214-4.06140.28021620.19672997315992
4.0614-4.2240.23611570.19862936309393
4.224-4.41610.22471480.19233012316092
4.4161-4.64870.21981370.20092887302490
4.6487-4.93960.22711620.18412956311893
4.9396-5.32050.21821480.18623040318894
5.3205-5.8550.22811600.18443103326395
5.855-6.70010.23481430.19333059320295
6.7001-8.43320.25321490.17043073322295
8.4332-46.46960.18961850.16812974315993

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