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- PDB-6zb8: Exo-beta-1,3-glucanase from moose rumen microbiome, active site m... -

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Basic information

Entry
Database: PDB / ID: 6zb8
TitleExo-beta-1,3-glucanase from moose rumen microbiome, active site mutant E167Q/E295Q
ComponentsExo-beta-1,3-glucanase variant E167Q/E295Q
KeywordsHYDROLASE / Glycoside hydrolase / Exo-beta-1 / 3-glucanase / family GH5_44 / active-site mutant
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 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 variant E167Q/E295Q
B: Exo-beta-1,3-glucanase variant E167Q/E295Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8194
Polymers90,7592
Non-polymers3,0602
Water11,241624
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 area3230 Å2
ΔGint-10 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.630, 87.790, 70.860
Angle α, β, γ (deg.)90.00, 100.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exo-beta-1,3-glucanase variant E167Q/E295Q


Mass: 45379.711 Da / Num. of mol.: 2 / Mutation: E167Q, E295Q
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
#2: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M TrisHCl pH 8.5, 0.2M MgCl, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.826561 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2019 / Details: Kirkpatrick-Baez mirror pair
RadiationMonochromator: Si (111), double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826561 Å / Relative weight: 1
ReflectionResolution: 1.35→29.35 Å / Num. obs: 139214 / % possible obs: 95.2 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rsym value: 0.084 / Net I/σ(I): 13.2
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10636 / CC1/2: 0.373 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Wild-type structure solved by MR-SAD

Resolution: 1.35→29.35 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.86
RfactorNum. reflection% reflection
Rfree0.1625 2000 1.44 %
Rwork0.1528 --
obs0.1529 139209 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 41 624 6753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086343
X-RAY DIFFRACTIONf_angle_d1.0078572
X-RAY DIFFRACTIONf_dihedral_angle_d19.0442368
X-RAY DIFFRACTIONf_chiral_restr0.077868
X-RAY DIFFRACTIONf_plane_restr0.0071084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38380.26271020.31027028X-RAY DIFFRACTION69
1.3838-1.42120.30821170.297974X-RAY DIFFRACTION78
1.4212-1.4630.281330.26929142X-RAY DIFFRACTION89
1.463-1.51020.27781480.237310162X-RAY DIFFRACTION99
1.5102-1.56420.22731490.209910196X-RAY DIFFRACTION100
1.5642-1.62680.20561490.187810227X-RAY DIFFRACTION100
1.6268-1.70080.19521490.178510243X-RAY DIFFRACTION100
1.7008-1.79050.17861500.161910299X-RAY DIFFRACTION100
1.7905-1.90270.15461500.147110258X-RAY DIFFRACTION100
1.9027-2.04950.16531490.134610282X-RAY DIFFRACTION100
2.0495-2.25570.14481510.129410332X-RAY DIFFRACTION100
2.2557-2.5820.14841500.131410289X-RAY DIFFRACTION100
2.582-3.25230.16381500.140710349X-RAY DIFFRACTION100

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