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- PDB-6r3r: First crystal structure of endo-levanase BT1760 from Bacteroides ... -

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Basic information

Entry
Database: PDB / ID: 6r3r
TitleFirst crystal structure of endo-levanase BT1760 from Bacteroides thetaiotaomicron
ComponentsGlycoside hydrolase family 32
KeywordsHYDROLASE / glycoside hydrolase 32 / 5-fold beta-propeller / beta-sandwich / levan hydrolysis
Function / homology
Function and homology information


beta-fructofuranosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
GH32, BT1760-like, C-terminal domain / GH32, BT1760-like, C-terminal domain / : / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-fructofuranosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsEek, P. / Ernits, K. / Lukk, T. / Alamae, T.
Funding support Estonia, 2items
OrganizationGrant numberCountry
Estonian Research CouncilPUT1050 Estonia
Estonian Research CouncilIUT19-9 Estonia
CitationJournal: Sci Rep / Year: 2019
Title: First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron.
Authors: Ernits, K. / Eek, P. / Lukk, T. / Visnapuu, T. / Alamae, T.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Glycoside hydrolase family 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,07814
Polymers57,9181
Non-polymers1,16013
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-38 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.657, 110.607, 171.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-603-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycoside hydrolase family 32


Mass: 57918.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1760 / Plasmid: pURI3-Cter / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6W6

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Non-polymers , 5 types, 472 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 3.22 Å3/Da / Density % sol: 61.8 % / Description: rod clusters
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32 mg/ml protein; 16-22% (w/v) PEG 6000, 1 mM ZnCl2, 0.1 M MES-NaOH, pH 6.5; 2:1 ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→29.8 Å / Num. obs: 87995 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 18.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Net I/σ(I): 16.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8685 / CC1/2: 0.765 / Rpim(I) all: 0.376 / Rrim(I) all: 0.857 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
AutoSolphasing
PHENIX1.15rc3-3435refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→29.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.171 1989 2.26 %
Rwork0.154 --
obs-87995 99.2 %
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 69 459 4466

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