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- PDB-5j7z: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi... -

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Basic information

Entry
Database: PDB / ID: 5j7z
TitleCrystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM1
ComponentsPutative secreted endoglycosylceramidase
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


endoglycosylceramidase / endoglycosylceramidase activity / galactosylceramide catabolic process / polysaccharide 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
Chem-18C / Endoglycoceramidase I / Endoglycoceramidase I
Similarity search - Component
Biological speciesRhodococcus equi 103S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionApr 7, 2016Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 27, 2016ID: 5DVG
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)109,3516
Polymers107,7402
Non-polymers1,6114
Water6,846380
1
A: Putative secreted endoglycosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4584
Polymers53,8701
Non-polymers1,5883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area17730 Å2
MethodPISA
2
B: Putative secreted endoglycosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8932
Polymers53,8701
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.283, 48.921, 120.227
Angle α, β, γ (deg.)90.00, 113.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative secreted endoglycosylceramidase


Mass: 53869.863 Da / Num. of mol.: 2 / Mutation: E339S
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
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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.: 1 / Source method: obtained synthetically / Formula: C36H71NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 48.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: PEG800 SODIUM HYDROXIDE AMMONIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 55310 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.25
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.485 / Rpim(I) all: 0.269

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CCU

5ccu


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.383 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2776 5.1 %RANDOM
Rwork0.167 ---
obs0.169 51963 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.05 Å2
2--0.29 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6801 0 95 380 7276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197118
X-RAY DIFFRACTIONr_bond_other_d0.0060.026494
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9629756
X-RAY DIFFRACTIONr_angle_other_deg1.333314935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34823.976327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82215976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2461547
X-RAY DIFFRACTIONr_chiral_restr0.080.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021638
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2452.3683546
X-RAY DIFFRACTIONr_mcbond_other1.2452.3673545
X-RAY DIFFRACTIONr_mcangle_it1.9853.5424429
X-RAY DIFFRACTIONr_mcangle_other1.9843.5434430
X-RAY DIFFRACTIONr_scbond_it1.8632.5713572
X-RAY DIFFRACTIONr_scbond_other1.8632.5713573
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0173.785329
X-RAY DIFFRACTIONr_long_range_B_refined4.33419.4868207
X-RAY DIFFRACTIONr_long_range_B_other4.33319.4848207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 200 -
Rwork0.18 3374 -
obs--87.23 %

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