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- PDB-2agc: Crystal Structure of mouse GM2- activator Protein -

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Basic information

Entry
Database: PDB / ID: 2agc
TitleCrystal Structure of mouse GM2- activator Protein
ComponentsGanglioside GM2 activator
KeywordsLIPID BINDING PROTEIN / constricted lipid binding pocket
Function / homology
Function and homology information


Glycosphingolipid catabolism / beta-N-acetylhexosaminidase activity / lipid storage / ganglioside catabolic process / nervous system process / oligosaccharide catabolic process / neuromuscular process controlling balance / Neutrophil degranulation / enzyme activator activity / learning or memory ...Glycosphingolipid catabolism / beta-N-acetylhexosaminidase activity / lipid storage / ganglioside catabolic process / nervous system process / oligosaccharide catabolic process / neuromuscular process controlling balance / Neutrophil degranulation / enzyme activator activity / learning or memory / lysosome / mitochondrion / membrane / cytosol
Similarity search - Function
Ganglioside M2 Activator Protein; Chain: A, / Ganglioside GM2 activator / Ganglioside GM2 activator / GM2-AP, lipid-recognition domain superfamily / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / MYRISTIC ACID / Ganglioside GM2 activator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWright, C.S. / Mi, L.Z. / Lee, S. / Rastinejad, F.
Citation
Journal: Biochemistry / Year: 2005
Title: Crystal Structure Analysis of Phosphatidylcholine-GM2-Activator Product Complexes: Evidence for Hydrolase Activity.
Authors: Wright, C.S. / Mi, L.Z. / Lee, S. / Rastinejad, F.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of Human GM2- Activator Protein with a Novel beta-cup Topology
Authors: Wright, C.S. / Li, S.C. / Rastinejad, F.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Structure Analysis of Lipid Complexes of GM2-Activator Protein
Authors: Wright, C.S. / Zhao, Q. / Rastinejad, F.
#3: Journal: J.Mol.Biol. / Year: 2004
Title: Evidence for Lipid Packaging in the Crystal Structure of the GM2-Activator Complex with Platelet Activating Factor
Authors: Wright, C.S. / Mi, L.Z. / Rastinejad, F.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1264
Polymers17,4971
Non-polymers6293
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.980, 51.270, 92.440
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 Ganglioside GM2 activator / GM2-AP


Mass: 17496.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gm2a / Organ: brain, kidney, liver / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q60648
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.76 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Peg 4000, acetate buffer , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 2, 1996 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 7535 / Num. obs: 7121 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.1 / Num. unique all: 738 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G13 monomer A

1g13


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 794095.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.299 765 10.8 %RANDOM
Rwork0.233 ---
obs0.233 7078 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.096 Å2 / ksol: 0.281038 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-12.21 Å20 Å20 Å2
2---2.63 Å20 Å2
3----9.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 44 66 1337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 119 10.5 %
Rwork0.298 1016 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4pc_myr_lpe_epe_lau.parampc_myr_lpe_epe_lau.top

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