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- PDB-4ghs: Crystal structure of human GLTP bound with 12:0 disulfatide (orth... -

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Basic information

Entry
Database: PDB / ID: 4ghs
TitleCrystal structure of human GLTP bound with 12:0 disulfatide (orthorombic form; two 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-0SG / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSamygina, V.R. / Popov, A.N. / Goni-de-Cerio, F. / Cabo-Bilbao, A. / 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 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 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
B: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3644
Polymers47,7562
Non-polymers1,6082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-18 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.948, 94.773, 130.799
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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C36H69NO14S2

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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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-20% PEG 3350, pH 7.0, 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: BRUKER AXS MICROSTAR / Detector: CCD / Date: Apr 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 11046 / Num. obs: 10751 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.2→3.31 Å / % possible all: 97.9

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Processing

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

3rzn


Resolution: 3.2→14.99 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.848 / SU B: 52.007 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R Free: 0.528 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27616 511 4.8 %RANDOM
Rwork0.19275 ---
obs0.19662 10110 97.92 %-
all-10110 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.626 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2---2.29 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 3.2→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 106 0 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223522
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.9192.0024766
X-RAY DIFFRACTIONr_angle_other_deg1.07136004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4465412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51824.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.71615612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3841512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7041.52084
X-RAY DIFFRACTIONr_mcbond_other0.0861.5826
X-RAY DIFFRACTIONr_mcangle_it1.33823376
X-RAY DIFFRACTIONr_scbond_it1.57631438
X-RAY DIFFRACTIONr_scangle_it2.8044.51390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 30 -
Rwork0.254 699 -
obs--97.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0035-0.7827-0.2354.56050.26481.3937-0.15060.04510.08340.53050.06460.02960.1440.06370.0860.24660.00250.08980.1781-0.02040.2503-20.81177.1773-27.2722
22.3131-1.4798-0.7581.92880.41020.74390.59780.20350.1002-0.5593-0.5458-0.0153-0.16450.1516-0.05190.31940.05880.06840.34330.03630.1593-12.4867-7.1256-53.1675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 209
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B3 - 209
4X-RAY DIFFRACTION2B301

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