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- PDB-6y6s: Mouse Galactocerebrosidase complexed with galacto-noeurostegine G... -

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Basic information

Entry
Database: PDB / ID: 6y6s
TitleMouse Galactocerebrosidase complexed with galacto-noeurostegine GNS at pH 6.8
ComponentsGalactocerebrosidase
KeywordsHYDROLASE / Inhibitor
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 / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Chem-ODW / Galactocerebrosidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDeane, J.E. / McLoughlin, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyUF100371 United Kingdom
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: The Bicyclic Form of galacto -Noeurostegine Is a Potent Inhibitor of beta-Galactocerebrosidase.
Authors: Viuff, A. / Salamone, S. / McLoughlin, J. / Deane, J.E. / Jensen, H.H.
History
DepositionFeb 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)76,3798
Polymers74,5971
Non-polymers1,7827
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint1 kcal/mol
Surface area24150 Å2
Unit cell
Length a, b, c (Å)248.721, 248.721, 77.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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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: Glycosylated protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Galc / 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 , 4 types, 270 molecules

#3: Chemical ChemComp-ODW / (1~{R},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-8-azabicyclo[3.2.1]octane-1,2,3-triol / galacto-noeurostegine / GNS


Mass: 189.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.09 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate (pH 6.8), and 34% wt/vol polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→124.36 Å / Num. obs: 53072 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 40.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 2623 / CC1/2: 0.461

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zr5

3zr5


Resolution: 2.1→56.07 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2062
RfactorNum. reflection% reflection
Rfree0.2013 2687 5.07 %
Rwork0.1634 --
obs0.1653 53021 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 15 267 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075403
X-RAY DIFFRACTIONf_angle_d0.84187377
X-RAY DIFFRACTIONf_chiral_restr0.0513796
X-RAY DIFFRACTIONf_plane_restr0.0048929
X-RAY DIFFRACTIONf_dihedral_angle_d10.49153042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.35241250.28552628X-RAY DIFFRACTION99.21
2.14-2.180.28281190.25652659X-RAY DIFFRACTION99.89
2.18-2.220.2661360.23332632X-RAY DIFFRACTION99.93
2.22-2.270.28891550.2282634X-RAY DIFFRACTION99.93
2.27-2.320.27161400.21962637X-RAY DIFFRACTION99.86
2.32-2.380.25231470.20762629X-RAY DIFFRACTION99.78
2.38-2.450.23641690.19292593X-RAY DIFFRACTION99.89
2.45-2.520.25281500.17972632X-RAY DIFFRACTION99.86
2.52-2.60.2291320.18432646X-RAY DIFFRACTION99.89
2.6-2.690.24121590.17452624X-RAY DIFFRACTION99.96
2.69-2.80.24381510.1742641X-RAY DIFFRACTION99.93
2.8-2.930.22741340.17892648X-RAY DIFFRACTION99.93
2.93-3.080.22921240.17922664X-RAY DIFFRACTION100
3.08-3.280.22271480.18652644X-RAY DIFFRACTION99.96
3.28-3.530.21281330.16782669X-RAY DIFFRACTION100
3.53-3.880.17881450.1442654X-RAY DIFFRACTION99.96
3.88-4.450.13391420.12312668X-RAY DIFFRACTION100
4.45-5.60.14421340.11952695X-RAY DIFFRACTION100
5.6-56.070.17961440.15612737X-RAY DIFFRACTION99.65
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)
11.96023943640.724454038023-0.4117611439331.656044676130.01391259714920.1387700534910.1101369278720.4724472585590.398914587002-0.512229213164-0.0498162862768-0.529175655829-0.419884323370.6913796490280.007458755405430.790867183843-0.4350318534930.1590381067020.9475046745320.1488725406820.57878265577489.8926150561109.6724787081.48880212854
20.761850190781-0.2450353539440.02705522077930.9417757072560.07001958386771.6052029410.02887655536160.05819536218420.123516425698-0.05061996996990.00771896483043-0.16670254509-0.2996525667280.456249270377-0.02599358691440.289592901732-0.177228770998-0.004530993256770.4027582886340.006114820260.34266473721574.483662096299.021406644922.2927432038
30.1154468961780.09399702679130.0201604735480.0981862190180.0301674360960.0177925708684-0.04754043532330.03829255662820.198248474948-0.0909837478870.0580192080961-0.348283090165-0.1960553845610.3109215442310.1500751475070.352062881412-0.442895401887-0.03284529578170.9073205510360.01573008871770.6792482313498.0287529636104.66088585827.0837104422
41.35561352747-0.1870143745650.466252417622.16268140357-0.5968985213511.826566800530.0707553133439-0.119393388059-0.06063982345990.2497174085470.0173987722566-0.2161325024570.1756480577180.494118109968-0.09416115740150.302221106364-0.0294785314813-0.1003912750370.513270512938-0.01767706484650.33430966608182.599319839477.425673456443.3788336615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 25:40 or resseq 338:452)
2X-RAY DIFFRACTION2chain A and resseq 41:337
3X-RAY DIFFRACTION3chain A and resseq 453:471
4X-RAY DIFFRACTION4chain A and resseq 472:668

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