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- PDB-5nbo: Bacteroides ovatus mixed linkage glucan PUL (MLGUL) GH16 -

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Basic information

Entry
Database: PDB / ID: 5nbo
TitleBacteroides ovatus mixed linkage glucan PUL (MLGUL) GH16
ComponentsGlycosyl hydrolase family 16
KeywordsHYDROLASE / Glycoside hydrolase / GH16
Function / homologyGlycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Glycosyl hydrolase family 16
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHemsworth, G.R. / Tamura, K. / Dejean, G. / Rogers, T.E. / Pudlo, N.A. / Urs, K. / Jain, N. / Martens, E.C. / Brumer, H. / Davies, G.J.
CitationJournal: Cell Rep / Year: 2017
Title: Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides.
Authors: Tamura, K. / Hemsworth, G.R. / Dejean, G. / Rogers, T.E. / Pudlo, N.A. / Urs, K. / Jain, N. / Davies, G.J. / Martens, E.C. / Brumer, H.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 16
B: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4284
Polymers61,3042
Non-polymers1242
Water6,359353
1
A: Glycosyl hydrolase family 16


Theoretical massNumber of molelcules
Total (without water)30,6521
Polymers30,6521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7763
Polymers30,6521
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.466, 60.801, 49.385
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycosyl hydrolase family 16


Mass: 30651.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02741 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LY25
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM MES pH 6 200 mM LiCl2 15-25% Peg-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→49.23 Å / Num. obs: 45483 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.053 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / Num. unique obs: 2726 / CC1/2: 0.669 / Rpim(I) all: 0.365 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4crq

4crq


Resolution: 1.8→49.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.699 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20414 2392 5.3 %RANDOM
Rwork0.1613 ---
obs0.16351 43072 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.97 Å2
2---0.51 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 8 353 4127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193868
X-RAY DIFFRACTIONr_bond_other_d0.0020.023382
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9155229
X-RAY DIFFRACTIONr_angle_other_deg0.99337880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2675472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71625.567194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61715641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.787156
X-RAY DIFFRACTIONr_chiral_restr0.120.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
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_it1.5651.6751894
X-RAY DIFFRACTIONr_mcbond_other1.5471.6731893
X-RAY DIFFRACTIONr_mcangle_it2.1942.4982364
X-RAY DIFFRACTIONr_mcangle_other2.2032.4992365
X-RAY DIFFRACTIONr_scbond_it2.6751.9521974
X-RAY DIFFRACTIONr_scbond_other2.6751.9521974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1712.812866
X-RAY DIFFRACTIONr_long_range_B_refined5.22620.1844350
X-RAY DIFFRACTIONr_long_range_B_other5.22520.1894351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 184 -
Rwork0.262 3204 -
obs--99.85 %

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