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

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Basic information

Entry
Database: PDB / ID: 6fwm
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-1,2-anhydro-mannose hydrolyzed by enzyme
ComponentsGlycosyl hydrolase family 71
KeywordsHYDROLASE
Function / homology
Function and homology information


alpha-mannosidase activity / 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 / alpha-D-glucopyranose / Chem-M96 / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsSobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. ...Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Lu, D. / Sollogoub, M. / Rovira, C. / Jimenez-Barbero, J. / Davies, G.J. / Williams, S.J.
Funding support United Kingdom, Australia, Spain, 7items
OrganizationGrant numberCountry
European Research Council322942 United Kingdom
Australian Research CouncilFT130100103 Australia
Australian Research CouncilDP120101396 Australia
Spanish Ministry of Economy and CompetitivenessCTQ2017-85496-P Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-64597-C2-1P Spain
Agency for Administration of University and Research2017SGR-1189 Spain
Generalitat de Catalunya2014SGR-987 Spain
Citation
Journal: Acs Cent.Sci. / Year: 2020
Title: An Epoxide Intermediate in Glycosidase Catalysis.
Authors: Sobala, L.F. / Speciale, G. / Zhu, S. / Raich, L. / Sannikova, N. / Thompson, A.J. / Hakki, Z. / Lu, D. / Shamsi Kazem Abadi, S. / Lewis, A.R. / Rojas-Cervellera, V. / Bernardo-Seisdedos, G. ...Authors: Sobala, L.F. / Speciale, G. / Zhu, S. / Raich, L. / Sannikova, N. / Thompson, A.J. / Hakki, Z. / Lu, D. / Shamsi Kazem Abadi, S. / Lewis, A.R. / Rojas-Cervellera, V. / Bernardo-Seisdedos, G. / Zhang, Y. / Millet, O. / Jimenez-Barbero, J. / Bennet, A.J. / Sollogoub, M. / Rovira, C. / Davies, G.J. / Williams, S.J.
#1: Journal: ChemRxiv / Year: 2019
Title: An Epoxide Intermediate in Glycosidase Catalysis
Authors: Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Lu, D. / ...Authors: Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Lu, D. / Sollogoub, M. / Rovira, C. / Jimenez-Barbero, J. / Davies, G.J. / Williams, S.J.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author / Item: _chem_comp.type
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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 / _entity.pdbx_description ..._chem_comp.name / _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 1.4Feb 3, 2021Group: Data collection / Database references / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / diffrn_source / pdbx_database_related / pdbx_related_exp_data_set
Item: _chem_comp.pdbx_synonyms / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.5Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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)44,3514
Polymers43,9341
Non-polymers4173
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint3 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.273, 108.273, 67.456
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-650-

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-M96 / (1~{S},2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 178.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O5
#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.: 380 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 3 M sodium acetate, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.28→76.56 Å / Num. obs: 100146 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 10.7
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.445 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4974 / CC1/2: 0.439 / Rpim(I) all: 0.65 / Rrim(I) all: 1.589 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALS1.0-0-g66ac5d4data reduction
Aimless0.5.21data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M17

5m17


Resolution: 1.28→76.56 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.853 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16424 4977 5 %RANDOM
Rwork0.13772 ---
obs0.13905 95118 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å20 Å2
2---0.85 Å20 Å2
3---1.69 Å2
Refinement stepCycle: 1 / Resolution: 1.28→76.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 27 380 3216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023305
X-RAY DIFFRACTIONr_bond_other_d0.0020.022894
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9484588
X-RAY DIFFRACTIONr_angle_other_deg1.03236781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4885449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45223.374163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02915516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5691521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213812
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02749
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_it1.3851.7251549
X-RAY DIFFRACTIONr_mcbond_other1.371.7231547
X-RAY DIFFRACTIONr_mcangle_it1.8012.5971963
X-RAY DIFFRACTIONr_mcangle_other1.8012.5991964
X-RAY DIFFRACTIONr_scbond_it1.7341.8641756
X-RAY DIFFRACTIONr_scbond_other1.7341.8641756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0982.7442583
X-RAY DIFFRACTIONr_long_range_B_refined3.01221.1433972
X-RAY DIFFRACTIONr_long_range_B_other2.70720.483887
X-RAY DIFFRACTIONr_rigid_bond_restr1.81936199
X-RAY DIFFRACTIONr_sphericity_free22.4995235
X-RAY DIFFRACTIONr_sphericity_bonded10.0256196
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 336 -
Rwork0.271 7019 -
obs--99.69 %

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