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- PDB-4gh0: Crystal structure of D48V mutant of human GLTP bound with 12:0 mo... -

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Basic information

Entry
Database: PDB / ID: 4gh0
TitleCrystal structure of D48V mutant of human GLTP bound with 12:0 monosulfatide
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 / PENTADECANE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSamygina, V.R. / Cabo-Bilbao, A. / 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 7, 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_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: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7983
Polymers23,8621
Non-polymers9362
Water3,621201
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5966
Polymers47,7242
Non-polymers1,8734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6420 Å2
ΔGint-24 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.984, 47.242, 62.193
Angle α, β, γ (deg.)90.00, 125.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycolipid transfer protein / GLTP


Mass: 23861.820 Da / Num. of mol.: 1 / Mutation: D48V
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.: 1 / Source method: obtained synthetically / Formula: C36H69NO11S
#3: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 3350, 0.1M MES pH 5.0, 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: Apr 14, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 69954 / Num. obs: 40558 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.35→1.4 Å / % possible all: 99.7

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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: 3S0I

3s0i


Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.702 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.064 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18078 1965 4.9 %RANDOM
Rwork0.15215 ---
all0.15359 40407 --
obs0.15359 38442 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.48 Å2
2---0.08 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 64 201 1876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221787
X-RAY DIFFRACTIONr_bond_other_d0.0020.021271
X-RAY DIFFRACTIONr_angle_refined_deg1.6022.0062414
X-RAY DIFFRACTIONr_angle_other_deg1.27333145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02524.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46815331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.354157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2220.2437
X-RAY DIFFRACTIONr_nbd_other0.1770.21307
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2898
X-RAY DIFFRACTIONr_nbtor_other0.0880.2846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0430.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.232
X-RAY DIFFRACTIONr_mcbond_it1.9111.51360
X-RAY DIFFRACTIONr_mcbond_other0.7291.5406
X-RAY DIFFRACTIONr_mcangle_it2.2521699
X-RAY DIFFRACTIONr_scbond_it3.3333889
X-RAY DIFFRACTIONr_scangle_it4.2294.5711
X-RAY DIFFRACTIONr_rigid_bond_restr1.83933794
X-RAY DIFFRACTIONr_sphericity_free5.7863201
X-RAY DIFFRACTIONr_sphericity_bonded4.12833015
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 124 -
Rwork0.195 2827 -
obs--99.6 %

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