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- PDB-2osx: Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex -

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Basic information

Entry
Database: PDB / ID: 2osx
TitleEndo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex
ComponentsEndoglycoceramidase II
KeywordsHYDROLASE / (alpha/beta)8 (TIM) barrel
Function / homology
Function and homology information


endoglycosylceramidase / endoglycosylceramidase activity / carbohydrate derivative catabolic process / lipid catabolic process / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily ...Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-16C / Endoglycoceramidase II
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCaines, M.E.C. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and Mechanistic Analyses of endo-Glycoceramidase II, a Membrane-associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-bound Forms.
Authors: Caines, M.E. / Vaughan, M.D. / Tarling, C.A. / Hancock, S.M. / Warren, R.A. / Withers, S.G. / Strynadka, N.C.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4368
Polymers52,0811
Non-polymers1,3567
Water10,773598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.801, 61.984, 102.846
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1028-

HOH

21A-1163-

HOH

DetailsThe biological assembly is believed to be a monomer.

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Endoglycoceramidase II


Mass: 52080.500 Da / Num. of mol.: 1 / Mutation: E351S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: M-777 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Tuner) / References: UniProt: O33853, endoglycosylceramidase
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 604 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-16C / N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE / C16-CERAMIDE / N-PALMITOYL-D-ERYTHRO-SPHINGOSINE / (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL / (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL


Mass: 537.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H67NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 44.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→31.734 Å / Num. obs: 171712 / % possible obs: 93.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 7.094 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 9.2
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 1.5 / Num. measured all: 99776 / Num. unique all: 23927 / Rsym value: 0.463 / % possible all: 89.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→46.23 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.633 / SU ML: 0.014 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.139 8690 5.1 %RANDOM
Rwork0.121 ---
obs0.122 171710 93.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.03 Å2
2---0.19 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.1→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 73 598 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223769
X-RAY DIFFRACTIONr_bond_other_d0.0020.022540
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9695190
X-RAY DIFFRACTIONr_angle_other_deg0.95536155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71223.333171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37415528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.931531
X-RAY DIFFRACTIONr_chiral_restr0.090.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_nbd_refined0.2120.2762
X-RAY DIFFRACTIONr_nbd_other0.2070.22884
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21890
X-RAY DIFFRACTIONr_nbtor_other0.090.21907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2388
X-RAY DIFFRACTIONr_metal_ion_refined0.130.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.228
X-RAY DIFFRACTIONr_mcbond_it1.1591.52337
X-RAY DIFFRACTIONr_mcbond_other0.5961.5944
X-RAY DIFFRACTIONr_mcangle_it1.74223778
X-RAY DIFFRACTIONr_scbond_it2.20631510
X-RAY DIFFRACTIONr_scangle_it2.9424.51392
X-RAY DIFFRACTIONr_rigid_bond_restr0.97536703
X-RAY DIFFRACTIONr_sphericity_free6.6783619
X-RAY DIFFRACTIONr_sphericity_bonded3.6836186
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 601 -
Rwork0.231 11509 -
obs-12110 89.7 %

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