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- PDB-2af9: Crystal Structure analysis of GM2-Activator protein complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2af9
TitleCrystal Structure analysis of GM2-Activator protein complexed with phosphatidylcholine
ComponentsGanglioside GM2 activator
KeywordsLIPID BINDING PROTEIN / lipid-protein complex / lipid acyl chain stacking
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
LAURIC ACID / ISOPROPYL ALCOHOL / MYRISTIC ACID / OLEIC ACID / Ganglioside GM2 activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 25, 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 1.3Aug 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_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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8597
Polymers17,8281
Non-polymers1,0326
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.120, 41.980, 114.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ganglioside GM2 activator / GM2-AP


Mass: 17827.557 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-MYR / MYRISTIC ACID


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


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Peg 4000, iso-propanol, Hepes, pH 5.5, 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: 0.97943 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 13297 / Num. obs: 13297 / % possible obs: 92.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 23.67 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 34
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2746 / Rsym value: 0.292 / % possible all: 65

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUB

1pub


Resolution: 2→18.5 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1020095.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1020 8.1 %RANDOM
Rwork0.222 ---
obs0.222 12607 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.1868 Å2 / ksol: 0.400895 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.02 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 2→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 64 123 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_mcangle_it3.872
X-RAY DIFFRACTIONc_scbond_it9.752
X-RAY DIFFRACTIONc_scangle_it8.382.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 169 7.8 %
Rwork0.212 1994 -
obs--100 %
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.paramlpc_ola_myr_lau_epe.top

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