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- PDB-6zb9: Exo-beta-1,3-glucanase from moose rumen microbiome, wild type -

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Basic information

Entry
Database: PDB / ID: 6zb9
TitleExo-beta-1,3-glucanase from moose rumen microbiome, wild type
ComponentsExo-beta-1,3-glucanase
KeywordsHYDROLASE / Glycoside hydrolase / exo-beta-1 / 3-glucanase / family GH5_44
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKalyani, D.C. / Reichenbach, T. / Aspeborg, H. / Divne, C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2017-03877 Sweden
CitationJournal: Enzyme.Microb.Technol. / Year: 2021
Title: A homodimeric bacterial exo-beta-1,3-glucanase derived from moose rumen microbiome shows a structural framework similar to yeast exo-beta-1,3-glucanases.
Authors: Kalyani, D.C. / Reichenbach, T. / Aspeborg, H. / Divne, C.
History
DepositionJun 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 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: Exo-beta-1,3-glucanase
B: Exo-beta-1,3-glucanase


Theoretical massNumber of molelcules
Total (without water)90,7632
Polymers90,7632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The dimeric state was confirmed deduced from gel filtration, chemical cross-linking, ThermoFluor, PISA analysis and from the crystal-structure analysis.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-11 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.580, 88.040, 70.810
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exo-beta-1,3-glucanase


Mass: 45381.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: An active-site loop is disordered in the model and has therefore not been modeled.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1R / References: glucan 1,3-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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 0.2 M MgCl2, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.072897 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072897 Å / Relative weight: 1
ReflectionResolution: 2.5→47.55 Å / Num. obs: 44159 / % possible obs: 96.8 % / Redundancy: 3.4 % / CC1/2: 0.983 / Net I/σ(I): 5.8
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 4164 / CC1/2: 0.359

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD-generated model

Resolution: 2.5→47.547 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 3889 8.81 %
Rwork0.197 --
obs0.2036 44152 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 0 0 6088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096304
X-RAY DIFFRACTIONf_angle_d1.0298535
X-RAY DIFFRACTIONf_dihedral_angle_d3.1055215
X-RAY DIFFRACTIONf_chiral_restr0.059868
X-RAY DIFFRACTIONf_plane_restr0.0061084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.53050.37781090.32911168X-RAY DIFFRACTION77
2.5305-2.56260.38981170.32671176X-RAY DIFFRACTION82
2.5626-2.59630.40281210.32021256X-RAY DIFFRACTION87
2.5963-2.63190.34931420.31421455X-RAY DIFFRACTION94
2.6319-2.66950.38921400.30711446X-RAY DIFFRACTION99
2.6695-2.70930.34391430.31041461X-RAY DIFFRACTION99
2.7093-2.75160.3881480.30471510X-RAY DIFFRACTION100
2.7516-2.79670.38341390.3021479X-RAY DIFFRACTION100
2.7967-2.8450.36221430.2791479X-RAY DIFFRACTION100
2.845-2.89670.33851400.28381476X-RAY DIFFRACTION99
2.8967-2.95240.3631360.26491443X-RAY DIFFRACTION99
2.9524-3.01260.27071380.24111442X-RAY DIFFRACTION99
3.0126-3.07810.31511400.23531469X-RAY DIFFRACTION95
3.0781-3.14970.30011420.23061476X-RAY DIFFRACTION99
3.1497-3.22850.29221430.23611474X-RAY DIFFRACTION100
3.2285-3.31570.34781400.22481435X-RAY DIFFRACTION99
3.3157-3.41330.31821470.22731493X-RAY DIFFRACTION100
3.4133-3.52340.32511450.19361487X-RAY DIFFRACTION99
3.5234-3.64930.26031440.18621480X-RAY DIFFRACTION99
3.6493-3.79540.25691360.16741416X-RAY DIFFRACTION97
3.7954-3.9680.26621420.15481476X-RAY DIFFRACTION99
3.968-4.17710.23141430.15081478X-RAY DIFFRACTION100
4.1771-4.43860.23821400.14291454X-RAY DIFFRACTION100
4.4386-4.7810.20671450.13811474X-RAY DIFFRACTION99
4.781-5.26160.24531410.14111454X-RAY DIFFRACTION98
5.2616-6.02170.2281410.15461471X-RAY DIFFRACTION100
6.0217-7.58170.18151420.16521459X-RAY DIFFRACTION98

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