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- PDB-5ngk: The endo-beta1,6-glucanase BT3312 -

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Basic information

Entry
Database: PDB / ID: 5ngk
TitleThe endo-beta1,6-glucanase BT3312
ComponentsGlucosylceramidase
KeywordsHYDROLASE / glycoside hydrolase / endo-beta1 / 6-clucanase / beta-1 / 6-glucan / Bacteroides / human gut microbiota / yeast glycan
Function / homology
Function and homology information


glucosylceramide catabolic process / glucosylceramidase activity / sphingolipid metabolic process / extracellular region / membrane
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glucosylceramidase / Glucosylceramidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBasle, A. / Temple, M. / Cuskin, F. / Lowe, E. / Gilbert, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT097907MA United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A Bacteroidetes locus dedicated to fungal 1,6-beta-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-beta-glucanase.
Authors: Temple, M.J. / Cuskin, F. / Basle, A. / Hickey, N. / Speciale, G. / Williams, S.J. / Gilbert, H.J. / Lowe, E.C.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
C: Glucosylceramidase


Theoretical massNumber of molelcules
Total (without water)165,9733
Polymers165,9733
Non-polymers00
Water10,935607
1
A: Glucosylceramidase


Theoretical massNumber of molelcules
Total (without water)55,3241
Polymers55,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase


Theoretical massNumber of molelcules
Total (without water)55,3241
Polymers55,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucosylceramidase


Theoretical massNumber of molelcules
Total (without water)55,3241
Polymers55,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.418, 156.001, 78.050
Angle α, β, γ (deg.)90.00, 100.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucosylceramidase / BT3312


Mass: 55324.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: ERS852430_01553 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A173SYZ2, UniProt: Q8A2J3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM Sodium Bromide 100 mM Bis Tris Propane pH 6.5 and 20 % PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→48.24 Å / Num. obs: 114209 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.996 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4871 / CC1/2: 0.466 / % possible all: 97.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIL

3ril


Resolution: 1.9→48.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.701 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22124 5560 4.9 %RANDOM
Rwork0.18187 ---
obs0.18379 108363 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.579 Å2
Baniso -1Baniso -2Baniso -3
1--4.42 Å2-0 Å2-0.43 Å2
2--3.21 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10808 0 0 607 11415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211075
X-RAY DIFFRACTIONr_bond_other_d0.0020.029777
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.93915049
X-RAY DIFFRACTIONr_angle_other_deg0.986322763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01451363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6424.726529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32151803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4321548
X-RAY DIFFRACTIONr_chiral_restr0.0940.21631
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022294
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1613.2765464
X-RAY DIFFRACTIONr_mcbond_other2.1593.2755463
X-RAY DIFFRACTIONr_mcangle_it3.1244.9016820
X-RAY DIFFRACTIONr_mcangle_other3.1244.9026821
X-RAY DIFFRACTIONr_scbond_it2.5313.5225611
X-RAY DIFFRACTIONr_scbond_other2.5313.5225611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8565.1858229
X-RAY DIFFRACTIONr_long_range_B_refined5.24738.17312777
X-RAY DIFFRACTIONr_long_range_B_other5.22238.06812693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 362 -
Rwork0.341 7243 -
obs--89.41 %

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