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- PDB-1pu5: GM2-activator Protein crystal structure -

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Basic information

Entry
Database: PDB / ID: 1pu5
TitleGM2-activator Protein crystal structure
ComponentsGanglioside GM2 activator
KeywordsLIPID BINDING PROTEIN / Beta cup / large lipid binding pocket / protein dynamics
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 / lipid storage / ganglioside catabolic process / Glycosphingolipid catabolism / oligosaccharide catabolic process / lipid transport ...sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / maintenance of location in cell / lipid transporter activity / lipid storage / ganglioside catabolic process / Glycosphingolipid catabolism / 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
Ganglioside GM2 activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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

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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
C: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9595
Polymers53,4833
Non-polymers4772
Water7,782432
1
A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0662
Polymers17,8281
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ganglioside GM2 activator


Theoretical massNumber of molelcules
Total (without water)17,8281
Polymers17,8281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0662
Polymers17,8281
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Ganglioside GM2 activator
hetero molecules

B: Ganglioside GM2 activator


Theoretical massNumber of molelcules
Total (without water)35,8933
Polymers35,6552
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1070 Å2
ΔGint-13 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.320, 86.130, 120.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ganglioside GM2 activator / GM2-AP / Cerebroside sulfate activator protein / Shingolipid activator protein 3 / SAP-3


Mass: 17827.557 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GM2A / 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Peg 4000, iso-propanol, Hepes buffer, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 51764 / Num. obs: 50312 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.515

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G13

1g13


Resolution: 1.9→7.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2018589.88 / Data cutoff high rms absF: 2018589.88 / 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
Rfree0.253 5076 10.1 %RANDOM
Rwork0.214 ---
all0.219 51764 --
obs0.214 50312 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 92.897 Å2 / ksol: 0.512718 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-8 Å
Luzzati sigma a0.17 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 30 432 4182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 759 9.6 %
Rwork0.252 7127 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPARPROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2EPE_CNS_PAR.TXTEPE_CNS_TOP.TXT
X-RAY DIFFRACTION3SOLVENT_REP.PARAMSOLVENT.TOP

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