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

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Basic information

Entry
Database: PDB / ID: 4gjq
TitleCrystal structure of human GLTP bound with 12:0 monosulfatide (orthorhombic form;two subunits in asymmetric unit)
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / GLTP-fold
Function / homology
Function and homology information


Glycosphingolipid biosynthesis / glycolipid transfer activity / lipid transfer activity / glycosphingolipid biosynthetic process / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress ...Glycosphingolipid biosynthesis / glycolipid transfer activity / lipid transfer activity / glycosphingolipid biosynthetic process / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / 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-CIS / HEXANE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCabo-Bilbao, A. / Goni-de-Cerio, F. / Samygina, V.R. / Ochoa-Lizarralde, B. / 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
DepositionAug 10, 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)49,6225
Polymers47,7562
Non-polymers1,8673
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-15 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.959, 95.474, 132.390
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-CIS / (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE / (2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL / CIS-TETRACOSENOYL SULFATIDE


Mass: 890.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H91NO11S
#3: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 % PEG 3350, 0.1M MES pH 7.0, 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 315r / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 43981 / Num. obs: 43517 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.12 Å / % possible all: 98.5

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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
Starting model: 3RZN

3rzn


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.363 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26033 2209 5.1 %RANDOM
Rwork0.21701 ---
obs0.2192 41407 98.3 %-
all-41480 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 104 267 3597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223408
X-RAY DIFFRACTIONr_bond_other_d0.0020.022379
X-RAY DIFFRACTIONr_angle_refined_deg1.7342.0014604
X-RAY DIFFRACTIONr_angle_other_deg1.22435850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26624.722144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61915593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8311512
X-RAY DIFFRACTIONr_chiral_restr0.10.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
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_refined0.2210.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7641.52014
X-RAY DIFFRACTIONr_mcbond_other0.2031.5797
X-RAY DIFFRACTIONr_mcangle_it1.40923268
X-RAY DIFFRACTIONr_scbond_it2.34831394
X-RAY DIFFRACTIONr_scangle_it3.7484.51336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 163 -
Rwork0.315 3005 -
obs--99.56 %
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)
10.50811.0823-0.60823.2938-1.16640.7663-0.22280.09790.0113-0.60640.2887-0.34640.2323-0.1642-0.06590.3035-0.05730.09740.21350.01120.245921.5148.64828.37
21.27922.7744-0.59366.173-1.31290.28030.589-0.1662-0.0221.2851-0.5869-0.0249-0.27170.1117-0.00210.4189-0.10850.02320.359-0.00680.139611.672-7.62353.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 209
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION1A401 - 533
4X-RAY DIFFRACTION1B801
5X-RAY DIFFRACTION2B8 - 209
6X-RAY DIFFRACTION2B700
7X-RAY DIFFRACTION2A534 - 535
8X-RAY DIFFRACTION2B802 - 932

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