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- PDB-1pub: GM2-activator Protein crystal structure -

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Basic information

Entry
Database: PDB / ID: 1pub
TitleGM2-activator Protein crystal structure
ComponentsGM2-activator protein
KeywordsLIPID BINDING PROTEIN / beta-cup / enlarge lipid binding pocket
Function / homology
Function and homology information


sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / maintenance of location in cell / ganglioside catabolic process / lipid transporter activity / glycosphingolipid catabolic process / oligosaccharide catabolic process / lipid storage / Glycosphingolipid catabolism / lipid transport ...sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / maintenance of location in cell / ganglioside catabolic process / lipid transporter activity / glycosphingolipid catabolic process / oligosaccharide catabolic process / lipid storage / Glycosphingolipid catabolism / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Ganglioside GM2 activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsWright, C.S. / Zhao, Q. / Rastinejad, F.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural analysis of lipid complexes of GM2-activator protein.
Authors: Wright, C.S. / Zhao, Q. / Rastinejad, F.
History
DepositionJun 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GM2-activator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3092
Polymers17,6041
Non-polymers7051
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.070, 42.420, 113.780
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 GM2-activator protein


Mass: 17604.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: derivative of pT7-7 / Plasmid: pT513 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17900
#2: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 21% Peg 4000, 0.1M 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: 1.54041 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 20, 1995 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54041 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 7099 / Num. obs: 7091 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 3.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.3 / Num. unique all: 680 / Rsym value: 0.75 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: monomer A of pdb entry 1G13

1g13


Resolution: 2.51→7.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 968320.3 / Data cutoff high rms absF: 968320.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 727 10.9 %RANDOM
Rwork0.209 ---
obs0.209 6640 98.1 %-
all-6897 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 102.349 Å2 / ksol: 0.390013 e/Å3
Displacement parametersBiso mean: 50.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.18 Å20 Å20 Å2
2---6.86 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.51→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 48 61 1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.911.5
X-RAY DIFFRACTIONc_mcangle_it5.812
X-RAY DIFFRACTIONc_scbond_it10.982
X-RAY DIFFRACTIONc_scangle_it10.352.5
LS refinement shellResolution: 2.51→2.65 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 102 10.7 %
Rwork0.356 849 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PA_XPLOR.PARAMPA_XPLOR.TOP
X-RAY DIFFRACTION3SOLVENT_REP.PARAMSOLVENT.TOP

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