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Basic information

Entry
Database: PDB / ID: 6q63
TitleBT0459
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / Glycoside hydrolase family 20 / complex N-glycans / microbiota / bacteroidetes
Function / homology
Function and homology information


: / beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Fn3 associated repeat / Fn3 associated / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain ...Fn3 associated repeat / Fn3 associated / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsBasle, A. / Crouch, L. / Bolam, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M029018/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci.
Authors: Briliute, J. / Urbanowicz, P.A. / Luis, A.S. / Basle, A. / Paterson, N. / Rebello, O. / Hendel, J. / Ndeh, D.A. / Lowe, E.C. / Martens, E.C. / Spencer, D.I.R. / Bolam, D.N. / Crouch, L.I.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Beta-hexosaminidase
B: Beta-hexosaminidase
C: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,71912
Polymers259,7453
Non-polymers9749
Water2,540141
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9064
Polymers86,5821
Non-polymers3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9064
Polymers86,5821
Non-polymers3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9064
Polymers86,5821
Non-polymers3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.842, 186.880, 242.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Beta-hexosaminidase


Mass: 86581.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: exo I_10, ERS852511_03057 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A174QSL3, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Cu
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.83 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, 100 mM Bis-Tris propane pH 7.5, 10 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.44→49.75 Å / Num. obs: 147443 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Net I/σ(I): 12.2
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.551 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
Cootmodel building
PARROTphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCN

3rcn


Resolution: 2.44→49.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 17.428 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23493 7654 5.2 %RANDOM
Rwork0.21068 ---
obs0.21194 139765 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.876 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--1.36 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2.44→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17880 0 6 141 18027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01318335
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716568
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.65124927
X-RAY DIFFRACTIONr_angle_other_deg1.0791.57838620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96352249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80523.686936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.005153024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4041575
X-RAY DIFFRACTIONr_chiral_restr0.0430.22394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023740
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_it0.5623.9029008
X-RAY DIFFRACTIONr_mcbond_other0.5623.9029007
X-RAY DIFFRACTIONr_mcangle_it0.9955.85211253
X-RAY DIFFRACTIONr_mcangle_other0.9955.85211254
X-RAY DIFFRACTIONr_scbond_it0.5473.9579327
X-RAY DIFFRACTIONr_scbond_other0.5473.9589328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9715.90913675
X-RAY DIFFRACTIONr_long_range_B_refined2.0343.61219114
X-RAY DIFFRACTIONr_long_range_B_other2.02743.60519104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 503 -
Rwork0.364 10306 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8696-0.49960.48790.7262-0.66480.80640.17090.1039-0.0483-0.2612-0.08060.02890.33190.0973-0.09030.14820.025-0.05710.04330.02480.072418.67651.554130.8414
21.8692-0.47660.10390.3507-0.26530.29740.0573-0.10240.56780.0928-0.0659-0.1879-0.07190.06840.00860.1287-0.0232-0.02480.08930.05140.31440.084467.023157.1499
30.4218-0.1035-0.39670.42391.07862.8329-0.1022-0.1039-0.17670.24240.2358-0.06480.69330.6716-0.13350.27030.18-0.02450.1958-0.06830.178751.094174.5112-0.4078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 903
2X-RAY DIFFRACTION2B24 - 903
3X-RAY DIFFRACTION3C24 - 903

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