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- PDB-2ag2: Crystal Structure Analysis of GM2-activator protein complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2ag2
TitleCrystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine
ComponentsGanglioside GM2 activator
KeywordsLIPID BINDING PROTEIN / phospholipid-protein complex / lipid acyl chain stacking / packaging
Function / homology
Function and homology information


sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / maintenance of location in cell / lipid transporter activity / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / lipid transport ...sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / maintenance of location in cell / lipid transporter activity / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / lipid transport / phospholipase activator activity / neuromuscular process controlling balance / 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
Chem-CH5 / LAURIC ACID / ISOPROPYL ALCOHOL / Chem-LP3 / 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 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: Non-polymer description / 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
B: Ganglioside GM2 activator
C: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,50429
Polymers53,4833
Non-polymers5,02126
Water10,701594
1
A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2717
Polymers17,8281
Non-polymers1,4436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,53710
Polymers17,8281
Non-polymers1,7109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,69612
Polymers17,8281
Non-polymers1,86811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.530, 86.190, 120.480
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, 3 molecules ABC

#1: Protein Ganglioside GM2 activator / GM2-AP


Mass: 17827.557 Da / Num. of mol.: 3
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 , 9 types, 620 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-LP3 / (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE


Mass: 524.691 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H55NO7P
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-CH5 / 2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM / GLYCERO-3-PHOSPHOCHOLINE


Mass: 258.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H21NO6P
#7: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#9: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Peg 4000, Hepes, isopropanol, pH 7.6, 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: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 62215 / Num. obs: 61655 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 22.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6131 / % possible all: 93.7

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1PU5

1pu5


Resolution: 2→19.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1945871.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2287 5 %RANDOM
Rwork0.188 ---
obs0.188 45347 99.8 %-
all-45389 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.443 Å2 / ksol: 0.319658 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 331 594 4639
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it2.411.5
X-RAY DIFFRACTIONc_mcangle_it3.422
X-RAY DIFFRACTIONc_scbond_it10.172
X-RAY DIFFRACTIONc_scangle_it7.252.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 380 5.1 %
Rwork0.192 7057 -
obs--99.9 %
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 DIFFRACTION4ola_lpc_myr_lau_epe_chl.paramola_lpc_myr_lau_epe_chl.top

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