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- PDB-2oyl: Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like imi... -

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Basic information

Entry
Database: PDB / ID: 2oyl
TitleEndo-glycoceramidase II from Rhodococcus sp.: cellobiose-like imidazole complex
ComponentsEndoglycoceramidase II
KeywordsHYDROLASE / (alpha/beta)8 (TIM) barrel
Function / homology
Function and homology information


endoglycosylceramidase / endoglycosylceramidase activity / carbohydrate derivative catabolic process / polysaccharide catabolic process / lipid catabolic 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 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-IDC / Endoglycoceramidase II
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCaines, M.E.C. / Strynadka, N.C.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system.
Authors: Caines, M.E. / Hancock, S.M. / Tarling, C.A. / Wrodnigg, T.M. / Stick, R.V. / Stutz, A.E. / Vasella, A. / Withers, S.G. / Strynadka, N.C.
History
DepositionFeb 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: 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 / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglycoceramidase II
B: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24610
Polymers104,2452
Non-polymers1,0018
Water15,295849
1
A: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7156
Polymers52,1231
Non-polymers5925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5314
Polymers52,1231
Non-polymers4083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.752, 93.246, 94.432
Angle α, β, γ (deg.)90.000, 98.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPROAA43 - 14534 - 136
21PROPROPROPROBB43 - 14534 - 136
32GLYGLYALAALAAA157 - 490148 - 481
42GLYGLYALAALABB157 - 490148 - 481

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Components

#1: Protein Endoglycoceramidase II


Mass: 52122.535 Da / Num. of mol.: 2
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: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-IDC / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside / 5-HYDROXYMETHYL-5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDIN-6YL-7,8-DIOL-GLUCOPYRANOSIDE / IMIDAZOLE-DERIVED CELLOBIOSE / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucoside / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl D-glucoside / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl glucoside


Type: D-saccharide / Mass: 362.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N2O9
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
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: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→66 Å / Num. obs: 85295 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.018 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / Num. measured all: 89817 / Num. unique all: 12409 / Rsym value: 0.39 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OSW

2osw


Resolution: 1.8→53.15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.407 / SU ML: 0.077 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4295 5 %RANDOM
Rwork0.174 ---
obs0.175 85266 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.838 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å2-0.04 Å2
2--0.54 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 66 849 7664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227045
X-RAY DIFFRACTIONr_bond_other_d0.0020.024666
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9639685
X-RAY DIFFRACTIONr_angle_other_deg0.8693.00111271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5423.727322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71115983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0811550
X-RAY DIFFRACTIONr_chiral_restr0.0640.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
X-RAY DIFFRACTIONr_nbd_refined0.1940.21414
X-RAY DIFFRACTIONr_nbd_other0.1930.25074
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23421
X-RAY DIFFRACTIONr_nbtor_other0.0850.23478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2681
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.216
X-RAY DIFFRACTIONr_mcbond_it0.461.54398
X-RAY DIFFRACTIONr_mcbond_other0.1461.51770
X-RAY DIFFRACTIONr_mcangle_it0.81527094
X-RAY DIFFRACTIONr_scbond_it1.10332802
X-RAY DIFFRACTIONr_scangle_it1.7014.52575
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5532 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.220.5
MEDIUM THERMAL0.932
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 300 -
Rwork0.224 5977 -
obs-6277 99.98 %

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