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- PDB-4ad5: Structure of the GH99 endo-alpha-mannosidase from Bacteroides xyl... -

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Basic information

Entry
Database: PDB / ID: 4ad5
TitleStructure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin and alpha-1,2-mannobiose
ComponentsGLYCOSYL HYDROLASE FAMILY 71
KeywordsHYDROLASE / ENDOMANNOSIDASE / GLYCOSIDE HYDROLASE / GH99 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE GLYCOSIDASE INHIBITION
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 / 1-DEOXYMANNOJIRIMYCIN / alpha-D-glucopyranose / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBACTEROIDES XYLANISOLVENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. ...Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stuetz, A.E. / Butters, T.D. / Williams, S.J. / Davies, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and Mechanistic Insight Into N-Glycan Processing by Endo-Alpha-Mannosidase.
Authors: Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stutz, A.E. / Butters, T.D. ...Authors: Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stutz, A.E. / Butters, T.D. / Williams, S.J. / Davies, G.J.
History
DepositionDec 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_symm_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)44,1654
Polymers43,4791
Non-polymers6863
Water8,089449
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.844, 108.844, 67.762
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-2193-

HOH

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Components

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


Mass: 43479.266 Da / Num. of mol.: 1
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
#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-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
#4: Chemical ChemComp-DMJ / 1-DEOXYMANNOJIRIMYCIN


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.33 Å3/Da / Density % sol: 47.33 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 2011 / Details: OSMICS MULTILAYER OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 31280 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 7.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG

Resolution: 1.9→39.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.965 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1360 5.1 %RANDOM
Rwork0.15813 ---
obs0.16052 25505 85.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 45 449 3313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9484093
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9965359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19323.288146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0771518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212337
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21554
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22046
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0110.0222996
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2071.9484093
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 91 -
Rwork0.246 1766 -
obs--80.01 %

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