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- PDB-6hmg: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -

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Basic information

Entry
Database: PDB / ID: 6hmg
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine)
ComponentsGlycosyl hydrolase family 71
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-GDQ / alpha-D-glucopyranose / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsSobala, L.F. / Lu, D. / Zhu, S. / Bernardo-Seisdedos, G. / Millet, O. / Zhang, Y. / Sollogoub, M. / Jimenez-Barbero, J. / Davies, G.J.
Funding support United Kingdom, Spain, 3items
OrganizationGrant numberCountry
European Research Council322942 United Kingdom
Spanish Ministry of Economy and CompetitivenessCTQ2017-85496-P Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-64597-C2-1P Spain
CitationJournal: Org.Lett. / Year: 2018
Title: From 1,4-Disaccharide to 1,3-Glycosyl Carbasugar: Synthesis of a Bespoke Inhibitor of Family GH99 Endo-alpha-mannosidase.
Authors: Lu, D. / Zhu, S. / Sobala, L.F. / Bernardo-Seisdedos, G. / Millet, O. / Zhang, Y. / Jimenez-Barbero, J. / Davies, G.J. / Sollogoub, M.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jul 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.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.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 2.3Feb 10, 2021Group: Database references / Structure summary / Category: chem_comp / pdbx_related_exp_data_set / Item: _chem_comp.pdbx_synonyms
Revision 2.4Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3324
Polymers43,9341
Non-polymers3983
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint4 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.772, 108.772, 67.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

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Components

#1: Protein Glycosyl hydrolase family 71


Mass: 43933.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria)
Gene: BXY_34140 / Plasmid: pET28a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6D1V7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GDQ / (1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol


Mass: 159.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3 M sodium acetate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.27→39.5 Å / Num. obs: 103773 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Net I/σ(I): 13.1
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5070 / CC1/2: 0.515 / Rpim(I) all: 0.55 / Rrim(I) all: 1.409 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSNovember 3, 2014data reduction
Aimless0.5.12data scaling
REFMAC5.8.0124phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M17

5m17


Resolution: 1.27→39.5 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.698 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15413 5172 5 %RANDOM
Rwork0.13232 ---
obs0.13342 98601 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.69 Å2
Refinement stepCycle: 1 / Resolution: 1.27→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 26 342 3177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133295
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172876
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6674572
X-RAY DIFFRACTIONr_angle_other_deg1.5151.5756738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8455443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82221.809188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33915516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8921522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023826
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02776
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_it1.4351.8041541
X-RAY DIFFRACTIONr_mcbond_other1.4341.8021539
X-RAY DIFFRACTIONr_mcangle_it1.8262.7181951
X-RAY DIFFRACTIONr_mcangle_other1.8262.721952
X-RAY DIFFRACTIONr_scbond_it1.9591.9271754
X-RAY DIFFRACTIONr_scbond_other1.9561.9271754
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2412.8382575
X-RAY DIFFRACTIONr_long_range_B_refined2.79221.2743895
X-RAY DIFFRACTIONr_long_range_B_other2.63120.7473823
X-RAY DIFFRACTIONr_rigid_bond_restr1.77436171
X-RAY DIFFRACTIONr_sphericity_free23.5555222
X-RAY DIFFRACTIONr_sphericity_bonded13.64656145
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 355 -
Rwork0.289 7234 -
obs--99.84 %

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