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- PDB-5jbk: Trichoderma harzianum GH1 beta-glucosidase ThBgl1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5jbk
TitleTrichoderma harzianum GH1 beta-glucosidase ThBgl1
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / GH1 / Trichoderma harzianum
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / 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
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsFlorindo, R.N. / Mutti, H.S. / Polikarpov, I. / Nascimento, A.S.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/56255-9 Brazil
Sao Paulo Research Foundation (FAPESP)2014/06565-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)485950/2013-8 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)490022/2009-0 Brazil
CitationJournal: N Biotechnol / Year: 2018
Title: Structural insights into beta-glucosidase transglycosylation based on biochemical, structural and computational analysis of two GH1 enzymes from Trichoderma harzianum.
Authors: Florindo, R.N. / Souza, V.P. / Mutti, H.S. / Camilo, C. / Manzine, L.R. / Marana, S.R. / Polikarpov, I. / Nascimento, A.S.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4914
Polymers106,3072
Non-polymers1842
Water8,971498
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-6 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.860, 97.722, 106.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-glucosidase /


Mass: 53153.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma harzianum (fungus) / Gene: THAR02_05432 / Plasmid: pET-Trx / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F9ZQA8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M hexahydrated magnesium chloride, 0.1M HEPES pH 7.5 and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 1, 2013
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 2.59→71.92 Å / Num. obs: 31180 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 17.46 Å2 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AHY

3ahy


Resolution: 2.593→71.92 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2539 1571 5.04 %
Rwork0.2134 --
obs0.2155 31180 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.593→71.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7453 0 12 498 7963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047698
X-RAY DIFFRACTIONf_angle_d0.63410470
X-RAY DIFFRACTIONf_dihedral_angle_d12.0494479
X-RAY DIFFRACTIONf_chiral_restr0.0421074
X-RAY DIFFRACTIONf_plane_restr0.0041372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5932-2.67690.31691340.27632573X-RAY DIFFRACTION97
2.6769-2.77250.32691370.26222678X-RAY DIFFRACTION100
2.7725-2.88350.31011360.26452672X-RAY DIFFRACTION100
2.8835-3.01480.31641340.25422663X-RAY DIFFRACTION100
3.0148-3.17370.28761660.25792655X-RAY DIFFRACTION100
3.1737-3.37260.25281190.23262693X-RAY DIFFRACTION100
3.3726-3.6330.29661350.22062681X-RAY DIFFRACTION100
3.633-3.99850.2341400.19812701X-RAY DIFFRACTION100
3.9985-4.5770.20941620.16622688X-RAY DIFFRACTION100
4.577-5.76620.19581570.15912743X-RAY DIFFRACTION100
5.7662-71.94660.19721510.16942862X-RAY DIFFRACTION100

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