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- PDB-6fwq: Structure of an E333Q variant of the GH99 endo-alpha-mannanase fr... -

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Entry
Database: PDB / ID: 6fwq
TitleStructure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-1,3-mannobiose and alpha-1,2-mannobiose
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
2alpha-alpha-mannobiose / 3alpha-alpha-mannobiose / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 7, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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 2.1Feb 3, 2021Group: Data collection / Database references / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / diffrn_source / pdbx_related_exp_data_set
Item: _chem_comp.pdbx_synonyms / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 2.2Jan 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)44,6404
Polymers43,9331
Non-polymers7083
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint5 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.651, 108.651, 68.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Glycosyl hydrolase family 71


Mass: 43932.609 Da / Num. of mol.: 1 / Mutation: E333Q
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: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 3 M sodium acetate, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.65→76.83 Å / Num. obs: 47947 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Net I/σ(I): 8.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2336 / CC1/2: 0.406 / Rpim(I) all: 0.578 / Rrim(I) all: 1.171 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia20.4.0.342-ge8fbd7c-dials-1.2data reduction
Aimless0.5.26data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M17

5m17


Resolution: 1.65→76.83 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.29 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18875 2376 5 %RANDOM
Rwork0.14633 ---
obs0.14846 45571 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å2-0 Å2
2--0.81 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.65→76.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 47 160 2968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023159
X-RAY DIFFRACTIONr_bond_other_d0.0020.022729
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.954373
X-RAY DIFFRACTIONr_angle_other_deg1.00836382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.715411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05623.333156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43115474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6511520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it2.4762.6171468
X-RAY DIFFRACTIONr_mcbond_other2.4752.6151467
X-RAY DIFFRACTIONr_mcangle_it3.0273.9221851
X-RAY DIFFRACTIONr_mcangle_other3.0273.9241852
X-RAY DIFFRACTIONr_scbond_it2.8212.7921691
X-RAY DIFFRACTIONr_scbond_other2.8212.7921691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3714.1072491
X-RAY DIFFRACTIONr_long_range_B_refined3.96229.3983492
X-RAY DIFFRACTIONr_long_range_B_other3.8829.1753469
X-RAY DIFFRACTIONr_rigid_bond_restr2.29835888
X-RAY DIFFRACTIONr_sphericity_free29.3375115
X-RAY DIFFRACTIONr_sphericity_bonded10.33455802
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 161 -
Rwork0.283 3350 -
obs--99.66 %

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