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- PDB-2e9m: Crystal Structure of human Cytosolic Neutral beta-Glycosylceramid... -

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Basic information

Entry
Database: PDB / ID: 2e9m
TitleCrystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Galactose and fatty acids
ComponentsCytosolic beta-glucosidase
KeywordsHYDROLASE / Novel Cytosolic Neutral beta-Glycosylceramidase
Function / homology
Function and homology information


glycosylceramidase activity / positive regulation of exo-alpha-sialidase activity / galactosylceramide catabolic process / glycosylceramide catabolic process / beta-glucoside catabolic process / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / glycosphingolipid catabolic process / glucosylceramide catabolic process ...glycosylceramidase activity / positive regulation of exo-alpha-sialidase activity / galactosylceramide catabolic process / glycosylceramide catabolic process / beta-glucoside catabolic process / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / glycosphingolipid catabolic process / glucosylceramide catabolic process / glucosylceramidase activity / glycoside catabolic process / : / Glycosphingolipid catabolism / oligosaccharide catabolic process / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / catalytic complex / protein stabilization / cytosol
Similarity search - Function
Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / OLEIC ACID / PALMITIC ACID / Cytosolic beta-glucosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKakuta, Y. / Hayashi, Y. / Okino, N. / Ito, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.
Authors: Hayashi, Y. / Okino, N. / Kakuta, Y. / Shikanai, T. / Tani, M. / Narimatsu, H. / Ito, M.
History
DepositionJan 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4704
Polymers53,7511
Non-polymers7193
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.244, 83.797, 93.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytosolic beta-glucosidase / Cytosolic Neutral beta-Glycosylceramidase / Klotho-related Protein / KLrP / Cytosolic beta- ...Cytosolic Neutral beta-Glycosylceramidase / Klotho-related Protein / KLrP / Cytosolic beta-glucosidase- like protein 1


Mass: 53751.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9H227, beta-glucosidase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 27.5% PEG3350, 0.1M Tris-HCl buffer, pH 8.5, 0.2M magnesium chloride, 5% glycerol, 0.5M galactose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2006
RadiationMonochromator: Si 111 CHANNE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 40776 / Num. obs: 40776 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 35.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 6.7 / Num. unique all: 4816 / Rsym value: 0.321 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E9L

2e9l


Resolution: 1.8→38.21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.87 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.176 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23642 2006 5 %RANDOM
Rwork0.20133 ---
all0.20315 38042 --
obs0.20315 38042 81.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 50 380 4212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9425361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26724.381194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0751515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21990
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22704
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5391.52385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89923758
X-RAY DIFFRACTIONr_scbond_it1.38131831
X-RAY DIFFRACTIONr_scangle_it2.1724.51599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 178 -
Rwork0.277 3385 -
obs--99.86 %

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