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- PDB-5nbp: Bacteroides ovatus mixed linkage glucan PUL (MLGUL) GH16 in compl... -

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Basic information

Entry
Database: PDB / ID: 5nbp
TitleBacteroides ovatus mixed linkage glucan PUL (MLGUL) GH16 in complex with G4G4G3G Product
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 / FOURIER SYNTHESIS / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)62,7419
Polymers61,3042
Non-polymers1,4377
Water4,720262
1
A: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4214
Polymers30,6521
Non-polymers7693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3215
Polymers30,6521
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.342, 60.149, 49.673
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 267 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM MES pH 6 200 mM LiCl2 15-25 % w/v PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→49.57 Å / Num. obs: 45347 / % possible obs: 99 % / Observed criterion σ(F): 0.094 / Redundancy: 3.9 % / CC1/2: 0.994 / Rpim(I) all: 0.066 / Net I/σ(I): 10.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2705 / CC1/2: 0.516 / Rpim(I) all: 0.499 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NBO

5nbo


Resolution: 1.8→49.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.121
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2384 5.3 %RANDOM
Rwork0.175 ---
obs0.1769 45346 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.65 Å2 / Biso mean: 22.191 Å2 / Biso min: 11.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20.78 Å2
2---0.78 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 93 262 4104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193960
X-RAY DIFFRACTIONr_bond_other_d00.023441
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9385369
X-RAY DIFFRACTIONr_angle_other_deg3.81338008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84225.487195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45515630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.071156
X-RAY DIFFRACTIONr_chiral_restr0.1020.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024386
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02816
X-RAY DIFFRACTIONr_mcbond_it1.3841.9971898
X-RAY DIFFRACTIONr_mcbond_other1.3791.9951897
X-RAY DIFFRACTIONr_mcangle_it2.0462.9842370
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 189 -
Rwork0.28 3155 -
all-3344 -
obs--98.91 %

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