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- PDB-1g13: HUMAN GM2 ACTIVATOR STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1g13
TitleHUMAN GM2 ACTIVATOR STRUCTURE
ComponentsGANGLIOSIDE M2 ACTIVATOR PROTEIN
KeywordsLigand Binding Protein / beta cup
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
Ganglioside GM2 activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWright, C.S. / Li, S.C. / Rastinejad, F.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and preliminary X-ray characterization of GM2-activator protein
Authors: Wright, C.S. / Li, S.-C.
History
DepositionOct 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / refine
Item: _refine.ls_percent_reflns_obs
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: GANGLIOSIDE M2 ACTIVATOR PROTEIN
B: GANGLIOSIDE M2 ACTIVATOR PROTEIN
C: GANGLIOSIDE M2 ACTIVATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3334
Polymers53,0943
Non-polymers2381
Water6,954386
1
A: GANGLIOSIDE M2 ACTIVATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9362
Polymers17,6981
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GANGLIOSIDE M2 ACTIVATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,6981
Polymers17,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GANGLIOSIDE M2 ACTIVATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,6981
Polymers17,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: GANGLIOSIDE M2 ACTIVATOR PROTEIN
hetero molecules

B: GANGLIOSIDE M2 ACTIVATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,6343
Polymers35,3962
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1020 Å2
ΔGint-13 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.420, 85.630, 120.070
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 M2 ACTIVATOR PROTEIN


Mass: 17698.096 Da / Num. of mol.: 3 / Fragment: RESIDUES 39-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: KIDNEY / Production host: Escherichia coli (E. coli) / References: UniProt: P17900
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, propanol, sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium HEPES1reservoir
220 %(v/v)PEG40001reservoir
310 %(v/v)propanol1reservoir
414 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979
DetectorType: ccd / Detector: CCD / Date: May 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 44590 / Num. obs: 44581 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 45.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.33 / Num. unique all: 4326 / % possible all: 99
Reflection
*PLUS
Num. measured all: 84502
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 2→6 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber / Details: torsion angle refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3866 9 %random
Rwork0.215 ---
all-43102 --
obs-42723 --
Solvent computationSolvent model: Least Squares / Bsol: 136.55 Å2 / ksol: 0.7133 e/Å3
Displacement parametersBiso mean: 34 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 15 386 4093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d26.13
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.34
X-RAY DIFFRACTIONc_mcangle_it2.03
X-RAY DIFFRACTIONc_scbond_it2.1
X-RAY DIFFRACTIONc_scangle_it2.94
LS refinement shellResolution: 2→6 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2629 266 0.0625 %
Rwork0.2181 2480 -
obs--0.645 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.13
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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