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- PDB-4ufj: Mouse Galactocerebrosidase complexed with iso-galacto-fagomine la... -

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Basic information

Entry
Database: PDB / ID: 4ufj
TitleMouse Galactocerebrosidase complexed with iso-galacto-fagomine lactam IGL
ComponentsGALACTOCEREBROSIDASE
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / COMPLEX / LYSOSOME
Function / homology
Function and homology information


Glycosphingolipid catabolism / galactosylceramide catabolic process / galactosylceramidase / galactosylceramidase activity / myelination / lysosome / mitochondrion / membrane
Similarity search - Function
Glycosyl hydrolase family 59, central domain / Glycosyl hydrolase family 59 central domain / Glycoside hydrolase, family 59 / : / Galactocerebrosidase, C-terminal lectin domain / : / Glycosyl hydrolase family 59 / Exo-inulinase; domain 1 / Glycosidases / Aldolase class I ...Glycosyl hydrolase family 59, central domain / Glycosyl hydrolase family 59 central domain / Glycoside hydrolase, family 59 / : / Galactocerebrosidase, C-terminal lectin domain / : / Glycosyl hydrolase family 59 / Exo-inulinase; domain 1 / Glycosidases / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-IF7 / Galactocerebrosidase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHill, C.H. / Viuff, A.H. / Spratley, S.J. / Salamone, S. / Christensen, S.H. / Read, R.J. / Moriarty, N.W. / Jensen, H.H. / Deane, J.E.
CitationJournal: Chem.Sci. / Year: 2015
Title: Azasugar Inhibitors as Pharmacological Chaperones for Krabbe Disease.
Authors: Hill, C.H. / Viuff, A.H. / Spratley, S.J. / Salamone, S. / Christensen, S.H. / Read, R.J. / Moriarty, N.W. / Jensen, H.H. / Deane, J.E.
History
DepositionMar 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALACTOCEREBROSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2927
Polymers74,5971
Non-polymers1,6966
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)249.850, 249.850, 77.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GALACTOCEREBROSIDASE / GALCERASE / GALACTOCEREBROSIDE BETA-GALACTOSIDASE / GALACTOSYLCERAMIDASE / GALACTOSYLCERAMIDE BETA- ...GALCERASE / GALACTOCEREBROSIDE BETA-GALACTOSIDASE / GALACTOSYLCERAMIDASE / GALACTOSYLCERAMIDE BETA-GALACTOSIDASE


Mass: 74596.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH IGL / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P54818, galactosylceramidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 198 molecules

#3: Chemical ChemComp-IF7 / (3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)piperidin-2-one / ISO-GALACTO-FAGOMINE LACTAM


Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNUMBERING IS FROM SECOND START SITE AS USED IN THE LITERATURE AND IN PDB ENTRIES 3ZR5, 3ZR6, 4CCC, 4CCD, 4CCE.

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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: 3.14 Å3/Da / Density % sol: 60.78 % / Description: NONE
Crystal growpH: 6.8
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.8), 34% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→63.2 Å / Num. obs: 46932 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 38.64 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZR5

3zr5


Resolution: 2.2→63.212 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 2421 5.2 %
Rwork0.1649 --
obs0.1666 46923 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→63.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 110 196 5423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055404
X-RAY DIFFRACTIONf_angle_d0.9327384
X-RAY DIFFRACTIONf_dihedral_angle_d11.6251866
X-RAY DIFFRACTIONf_chiral_restr0.053795
X-RAY DIFFRACTIONf_plane_restr0.004931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2450.30941370.2682605X-RAY DIFFRACTION100
2.245-2.29390.26591510.25112611X-RAY DIFFRACTION100
2.2939-2.34720.27921460.23772573X-RAY DIFFRACTION100
2.3472-2.40590.28561430.22472606X-RAY DIFFRACTION100
2.4059-2.4710.26481660.20452591X-RAY DIFFRACTION100
2.471-2.54370.22361440.20182576X-RAY DIFFRACTION100
2.5437-2.62580.23811360.20212610X-RAY DIFFRACTION100
2.6258-2.71960.21561520.19082599X-RAY DIFFRACTION100
2.7196-2.82850.26351540.18722607X-RAY DIFFRACTION100
2.8285-2.95730.19561200.18472631X-RAY DIFFRACTION100
2.9573-3.11320.19291320.1882641X-RAY DIFFRACTION100
3.1132-3.30820.22541460.18922590X-RAY DIFFRACTION100
3.3082-3.56360.21861270.17152656X-RAY DIFFRACTION100
3.5636-3.92220.19031490.14442606X-RAY DIFFRACTION100
3.9222-4.48960.1471370.12482636X-RAY DIFFRACTION100
4.4896-5.65590.12891360.11712658X-RAY DIFFRACTION100
5.6559-63.2380.17091450.1432706X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1661-0.42430.38582.7115-0.38382.10560.0527-0.2458-0.11520.32060.0547-0.30950.08570.5006-0.09310.3-0.0567-0.10460.53060.02890.385882.811377.918143.6707
20.46370.3259-0.16120.162-0.02960.24640.08740.27790.1490.1727-0.0628-0.3597-0.18550.97440.07850.3613-0.50470.02861.0290.11790.687798.4615105.181427.2934
31.3566-0.44870.18461.0321-0.00062.21990.06360.07430.0779-0.0405-0.0395-0.1824-0.32240.4747-0.02280.2942-0.1742-0.00120.36460.01330.301874.846499.511222.4026
42.34141.0835-0.16571.51470.71671.27690.14090.68170.3752-0.6058-0.1044-0.3717-0.64760.8531-0.05160.8104-0.4450.16871.04320.18430.557190.2595110.20331.445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 472:668)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 453:471)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 41:337)
4X-RAY DIFFRACTION4CHAIN A AND ((RESSEQ 25:40) OR (RESSEQ 338:452))

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