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- PDB-5j14: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi... -

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Basic information

Entry
Database: PDB / ID: 5j14
TitleCrystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM3
ComponentsPutative secreted endoglycosylceramidase
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


endoglycosylceramidase / endoglycosylceramidase activity / galactosylceramide catabolic process / extracellular region / membrane
Similarity search - Function
Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-lactose / Chem-18C / Endoglycoceramidase I / Endoglycoceramidase I
Similarity search - Component
Biological speciesRhodococcus equi 103S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.915 Å
AuthorsChen, L.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases
Authors: Han, Y.B. / Chen, L.Q. / Li, Z. / Tan, Y.M. / Feng, Y. / Yang, G.Y.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative secreted endoglycosylceramidase
B: Putative secreted endoglycosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8938
Polymers107,7402
Non-polymers2,1546
Water12,737707
1
A: Putative secreted endoglycosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0924
Polymers53,8701
Non-polymers1,2223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-2 kcal/mol
Surface area18550 Å2
MethodPISA
2
B: Putative secreted endoglycosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8014
Polymers53,8701
Non-polymers9313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint2 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.521, 49.053, 120.135
Angle α, β, γ (deg.)90.00, 114.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative secreted endoglycosylceramidase


Mass: 53869.863 Da / Num. of mol.: 2 / Mutation: E347S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus equi 103S (bacteria) / Strain: 103S / Gene: REQ_38260
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: E4W8N9, UniProt: A0A3S5YBC7*PLUS

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Sugars , 2 types, 2 molecules

#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
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 711 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-18C / N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE / C18-CERAMIDE / N-STEAROYL-D-ERYTHRO-SPHINGOSINE / (2S,3R,4E)-2-STEAROYLAMINOOCTADEC-4-ENE-1,3-DIOL / (2S,3R,4E)-2-STEAROYLAMINO-1,3-OCTADEC-4-ENEDIOL


Mass: 565.954 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H71NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 800, sodium hydroxide, ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.915→50 Å / Num. obs: 79432 / % possible obs: 97.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
REFMAC5.8.0009refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CCU

5ccu


Resolution: 1.915→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2043 --
Rwork0.1671 --
obs-79428 99.9585 %
Refinement stepCycle: LAST / Resolution: 1.915→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6789 0 146 707 7642
LS refinement shellResolution: 1.9153→1.9838 Å /
Rfactor% reflection
Rfree0.2539 -
Rwork0.1958 -
obs-93 %

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