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- PDB-4gxg: Crystal structure of human GLTP bound with 12:0 monosulfatide (or... -

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Basic information

Entry
Database: PDB / ID: 4gxg
TitleCrystal structure of human GLTP bound with 12:0 monosulfatide (orthorhombic form; four subunits in asymmetric unit)
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-EIS / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSamygina, V.R. / Cabo-Bilbao, A. / Goni-de-Cerio, F. / Popov, A.N. / 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
DepositionSep 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Glycolipid transfer protein
D: Glycolipid transfer protein
E: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4078
Polymers95,5114
Non-polymers2,8964
Water4,414245
1
A: Glycolipid transfer protein
B: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2044
Polymers47,7562
Non-polymers1,4482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area19330 Å2
MethodPISA
2
D: Glycolipid transfer protein
E: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2044
Polymers47,7562
Non-polymers1,4482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.205, 84.654, 171.876
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
Glycolipid transfer protein / GLTP


Mass: 23877.777 Da / Num. of mol.: 4
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-EIS / N-{(2S,3R,4E)-3-hydroxy-1-[(3-O-sulfo-beta-D-galactopyranosyl)oxy]octadec-4-en-2-yl}dodecanamide


Mass: 723.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H69NO11S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-20% PEG3350, pH7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9754 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 37037 / Num. obs: 37037 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.5 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / SU B: 9.685 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.532 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27064 1822 4.9 %RANDOM
Rwork0.20679 ---
all0.20992 36522 --
obs0.20992 35215 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6682 0 192 245 7119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227082
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9959541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25424.935308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1481524
X-RAY DIFFRACTIONr_chiral_restr0.120.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025136
X-RAY DIFFRACTIONr_nbd_refined0.2170.23581
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.25
X-RAY DIFFRACTIONr_mcbond_it0.6781.54291
X-RAY DIFFRACTIONr_mcangle_it1.13726750
X-RAY DIFFRACTIONr_scbond_it1.64733179
X-RAY DIFFRACTIONr_scangle_it2.5764.52791
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 121 -
Rwork0.265 2289 -
obs--89.82 %

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