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

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Basic information

Entry
Database: PDB / ID: 5ccu
TitleCrystal structure of endoglycoceramidase I from Rhodococ-cus equi
ComponentsPutative secreted endoglycosylceramidase
KeywordsHYDROLASE / Apo
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
Endoglycoceramidase I / Endoglycoceramidase I
Similarity search - Component
Biological speciesRhodococcus equi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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
DepositionJul 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,02622
Polymers107,8242
Non-polymers1,20220
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint31 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.841, 48.980, 120.304
Angle α, β, γ (deg.)90.00, 114.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative secreted endoglycosylceramidase


Mass: 53911.898 Da / Num. of mol.: 2 / Fragment: UNP residues 27-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus equi (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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 467 / 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: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 6000 MES 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 315r / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.108→50 Å / Num. obs: 58536 / % possible obs: 98.4 % / Redundancy: 4.2 % / Net I/σ(I): 10.09
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / % possible all: 96

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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: 2OSW

2osw


Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.754 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2943 5 %RANDOM
Rwork0.184 ---
obs0.186 55593 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.91 Å2
2---0.63 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 0 77 467 7347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197076
X-RAY DIFFRACTIONr_bond_other_d0.0020.026536
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9549650
X-RAY DIFFRACTIONr_angle_other_deg0.746315003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65523.914327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26515980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5451548
X-RAY DIFFRACTIONr_chiral_restr0.0590.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021634
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_it0.6192.153534
X-RAY DIFFRACTIONr_mcbond_other0.6192.153533
X-RAY DIFFRACTIONr_mcangle_it1.1223.2184407
X-RAY DIFFRACTIONr_mcangle_other1.1223.2194408
X-RAY DIFFRACTIONr_scbond_it0.6382.2273542
X-RAY DIFFRACTIONr_scbond_other0.6382.2273542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1293.2935244
X-RAY DIFFRACTIONr_long_range_B_refined3.13217.5988197
X-RAY DIFFRACTIONr_long_range_B_other3.13217.68198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 203 -
Rwork0.223 3807 -
obs--90.81 %

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