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- PDB-4utf: Structure of the GH99 endo-alpha-mannosidase from Bacteroides xyl... -

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Basic information

Entry
Database: PDB / ID: 4utf
TitleStructure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine and alpha- 1,2-mannobiose
ComponentsGLYCOSYL HYDROLASE FAMILY 71
KeywordsHYDROLASE / BACTEROIDES / ALPHA-MANNOSIDASE / POLYSACCHARIDE UTILISATION LOCUS / MANNOSE / MANNAN / BIOCATALYSIS / YEAST / CATALYTIC DOMAIN / CARBOHYDRATE CONFORMATION / CAZY / GLYCOSIDE HYDROLASE
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
2alpha-alpha-mannobiose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / alpha-D-mannopyranose / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBACTEROIDES XYLANISOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Pudlo, N.A. / Cameron, E.A. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. ...Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Pudlo, N.A. / Cameron, E.A. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Tolbert, T. / Piens, K. / Bracke, D. / Vervecken, W. / Hakki, Z. / Speciale, G. / Munoz-Munoz, J.L. / Pena, M.J. / McLean, R. / Suits, M.D. / Boraston, A.B. / Atherly, T. / Ziemer, C.J. / Williams, S.J. / Davies, G.J. / Abbott, D.W. / Martens, E.C. / Gilbert, H.J.
CitationJournal: Nature / Year: 2015
Title: Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism.
Authors: Cuskin, F. / Lowe, E.C. / Temple, M. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, T. ...Authors: Cuskin, F. / Lowe, E.C. / Temple, M. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, T.J. / Piens, K. / Bracke, D. / Vervecken, W. / Hakki, Z. / Speciale, G. / Munoz-Munoz, J.L. / Day, A. / Pena, M.J. / Mclean, R. / Suits, M.D.L. / Boraston, A.B. / Atherly, T. / Ziemer, C.J. / Williams, S.J. / Davies, G.J. / Abbott, W.D. / Martens, E.C. / Gilbert, H.J.
History
DepositionJul 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Non-polymer description
Revision 1.2Aug 10, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / 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_database_status / 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_special_symmetry / 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_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 / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 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: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2736
Polymers43,4791
Non-polymers7945
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.469, 108.469, 67.755
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-2081-

HOH

21A-2228-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GLYCOSYL HYDROLASE FAMILY 71 / ENDO-ALPHA-MANNOSIDASE


Mass: 43479.266 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES XYLANISOLVENS (bacteria) / Strain: XB1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: D6D1V7, glycoprotein endo-alpha-1,2-mannosidase

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Sugars , 2 types, 2 molecules

#2: 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
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 500 molecules

#4: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.2 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6.6 / Details: 2.8 M SODIUM ACETATE, PH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→39.4 Å / Num. obs: 96371 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 6.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED NATIVE APO STRUCTURE

Resolution: 1.3→76.7 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.31 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.13901 4797 5 %RANDOM
Rwork0.11196 ---
obs0.11333 91564 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.3→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 52 497 3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023118
X-RAY DIFFRACTIONr_bond_other_d0.0010.022786
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.954275
X-RAY DIFFRACTIONr_angle_other_deg1.22136424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05523.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29915467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7711520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213567
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02783
X-RAY DIFFRACTIONr_nbd_refined0.2510.21128
X-RAY DIFFRACTIONr_nbd_other0.190.22588
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21488
X-RAY DIFFRACTIONr_nbtor_other0.0850.21507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0860.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.284
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1461.7111462
X-RAY DIFFRACTIONr_mcbond_other2.1461.7111463
X-RAY DIFFRACTIONr_mcangle_it2.72.5761839
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3751.8491656
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6562.692420
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.42335903
X-RAY DIFFRACTIONr_sphericity_free37.5625149
X-RAY DIFFRACTIONr_sphericity_bonded9.58256143
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 354 -
Rwork0.233 6766 -
obs--99.93 %

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