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- PDB-5m5d: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -

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Basic information

Entry
Database: PDB / ID: 5m5d
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-D-glucal
ComponentsGlycosyl hydrolase family 71
KeywordsHYDROLASE / endomannanase / GH99 / inhibitor / D-glucal
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 / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsPetricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Rovira, C. ...Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / 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 CompetitivenessCTQ2014-55174 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-64597-C2-1P Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-68756-R Spain
Generalitat de Catalunya2014SGR-987 Spain
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
Authors: Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Jimenez-Barbero, J. / Rovira, C. / Davies, G.J. / Williams, S.J.
History
DepositionOct 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
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 / 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 / struct_asym / struct_conn / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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_alt_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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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 2.1Feb 10, 2021Group: Database references / Structure summary / Category: chem_comp / pdbx_related_exp_data_set / Item: _chem_comp.pdbx_synonyms
Revision 2.2Jan 17, 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)44,6118
Polymers43,9341
Non-polymers6787
Water7,188399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint22 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.684, 108.684, 67.641
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: 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: Polysaccharide alpha-D-mannopyranose-(1-3)-D-glucal


Type: oligosaccharide / Mass: 308.282 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[zz122h_1-5][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1,2-deoxy-Glcp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 3 M sodium acetate, pH 7.2

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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: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.07→76.85 Å / Num. obs: 172107 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.9
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.748 / Mean I/σ(I) obs: 0.6 / CC1/2: 0.33 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DIALS1.0-0-g66ac5d4data reduction
Aimless0.5.21data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified 4UTF

4utf


Resolution: 1.07→76.85 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.853 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1412 8530 5 %RANDOM
Rwork0.12438 ---
obs0.12522 163577 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.07→76.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 45 399 3237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023344
X-RAY DIFFRACTIONr_bond_other_d0.0030.023014
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9474633
X-RAY DIFFRACTIONr_angle_other_deg1.38737001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0365453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04723.114167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11215525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5811524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213926
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02850
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_it1.1341.5751553
X-RAY DIFFRACTIONr_mcbond_other1.1171.5731551
X-RAY DIFFRACTIONr_mcangle_it1.4982.3771971
X-RAY DIFFRACTIONr_mcangle_other1.5032.3791972
X-RAY DIFFRACTIONr_scbond_it1.5791.7421791
X-RAY DIFFRACTIONr_scbond_other1.5791.7421791
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8222.5492616
X-RAY DIFFRACTIONr_long_range_B_refined2.92919.1553920
X-RAY DIFFRACTIONr_long_range_B_other2.44518.5663854
X-RAY DIFFRACTIONr_rigid_bond_restr1.61736358
X-RAY DIFFRACTIONr_sphericity_free28.7695300
X-RAY DIFFRACTIONr_sphericity_bonded7.50456313
LS refinement shellResolution: 1.071→1.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 600 -
Rwork0.313 11840 -
obs--97.57 %

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