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- PDB-4gix: Crystal structure of human GLTP bound with 12:0 disulfatide -

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Basic information

Entry
Database: PDB / ID: 4gix
TitleCrystal structure of human GLTP bound with 12:0 disulfatide
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / GLTP-fold
Function / homology
Function and homology information


glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / glycolipid binding / Glycosphingolipid transport / intermembrane lipid transfer / response to immobilization stress / lipid binding ...glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / glycolipid binding / Glycosphingolipid transport / intermembrane lipid transfer / response to immobilization stress / lipid binding / identical protein binding / cytosol
Similarity search - Function
Glycolipid transfer protein domain / Glycolipid transfer protein superfamily / Glycolipid transfer protein (GLTP) / Glycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0SG / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSamygina, V.R. / Ochoa-Lizarralde, B. / Malinina, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insights into lipid-dependent reversible dimerization of human GLTP.
Authors: Samygina, V.R. / Ochoa-Lizarralde, B. / Popov, A.N. / Cabo-Bilbao, A. / Goni-de-Cerio, F. / Molotkovsky, J.G. / Patel, D.J. / Brown, R.E. / Malinina, L.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6822
Polymers23,8781
Non-polymers8041
Water2,882160
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3644
Polymers47,7562
Non-polymers1,6082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1750 Å2
ΔGint-16 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.768, 50.163, 65.850
Angle α, β, γ (deg.)90.00, 118.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

#1: Protein Glycolipid transfer protein / GLTP


Mass: 23877.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2
#2: Chemical ChemComp-0SG / N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide


Mass: 804.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H69NO14S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15%PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19652 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RZN

3rzn


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.02 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.142 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25053 949 4.9 %RANDOM
Rwork0.18345 ---
all0.18663 19825 --
obs0.18663 18508 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.389 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.65 Å2
2---1.1 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 53 160 1881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221790
X-RAY DIFFRACTIONr_bond_other_d0.0010.021249
X-RAY DIFFRACTIONr_angle_refined_deg1.3832.0022419
X-RAY DIFFRACTIONr_angle_other_deg1.33133084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0975206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2732578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.953156
X-RAY DIFFRACTIONr_chiral_restr0.080.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined0.2310.2423
X-RAY DIFFRACTIONr_nbd_other0.1820.21271
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2884
X-RAY DIFFRACTIONr_nbtor_other0.0870.2833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.222
X-RAY DIFFRACTIONr_mcbond_it1.0841.51371
X-RAY DIFFRACTIONr_mcbond_other0.2061.5411
X-RAY DIFFRACTIONr_mcangle_it1.17621694
X-RAY DIFFRACTIONr_scbond_it2.063882
X-RAY DIFFRACTIONr_scangle_it2.8914.5725
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 59 -
Rwork0.234 1317 -
obs--96.63 %

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