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- PDB-2ag9: Crystal Structure of the Y137S mutant of GM2-Activator Protein -

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Basic information

Entry
Database: PDB / ID: 2ag9
TitleCrystal Structure of the Y137S mutant of GM2-Activator Protein
ComponentsGanglioside GM2 activator
KeywordsLIPID BINDING PROTEIN / conformational changes in mobile loop (W131 loop)
Function / homology
Function and homology information


sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / lipid transporter activity / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / phospholipase activator activity / neuromuscular process controlling balance ...sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / lipid transporter activity / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / phospholipase activator activity / neuromuscular process controlling balance / lipid transport / lysosomal lumen / cytoplasmic side of plasma membrane / azurophil granule lumen / basolateral plasma membrane / learning or memory / apical plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / extracellular region / 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
ISOPROPYL ALCOHOL / MYRISTIC ACID / Ganglioside GM2 activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
B: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,57317
Polymers35,5032
Non-polymers1,07015
Water5,026279
1
A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,35211
Polymers17,7511
Non-polymers60110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2206
Polymers17,7511
Non-polymers4695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.490, 48.390, 55.590
Angle α, β, γ (deg.)76.16, 87.70, 87.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ganglioside GM2 activator / GM2-AP


Mass: 17751.461 Da / Num. of mol.: 2 / Mutation: Y137S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GM2A / Organ: LIVER, BRAIN, NEURONS / Plasmid: pET16b (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17900
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.04 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: Peg 4000, Hepes buffer, isopropanol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.92015 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92015 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 28299 / Num. obs: 18838 / % possible obs: 66.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 1.7 / % possible all: 26

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AG4

2ag4


Resolution: 2.2→19.87 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1051432.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1377 8.4 %RANDOM
Rwork0.243 ---
obs0.243 16410 77.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.4487 Å2 / ksol: 0.21949 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.19 Å20.52 Å20.53 Å2
2--6.28 Å26.63 Å2
3----1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 16 335 2835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.443 83 7.5 %
Rwork0.406 1025 -
obs--31.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3solvent_rep.paramsolvent.top
X-RAY DIFFRACTION4lpc_ola_myr_lau_epe.paramste_lpc_myr_lau_epe.top

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