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

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Basic information

Entry
Database: PDB / ID: 4gxd
TitleCrystal structure of D48V mutant 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 transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress ...glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid 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-0SG / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSamygina, 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
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_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

Downloads & links

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Assembly

Deposited unit
A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6662
Polymers23,8621
Non-polymers8041
Water73941
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3324
Polymers47,7242
Non-polymers1,6082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area2200 Å2
ΔGint-21 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.253, 47.317, 63.887
Angle α, β, γ (deg.)90.00, 126.07, 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-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.: 41 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% 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: ID2 / Wavelength: 0.9754 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 12893 / Num. obs: 12893 / % possible obs: 99.95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.15 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→14.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.506 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.264 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24878 544 4.9 %RANDOM
Rwork0.18308 ---
all0.2042 11145 --
obs0.18634 10595 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å20.54 Å2
2---1.79 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 53 41 1704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021707
X-RAY DIFFRACTIONr_bond_other_d0.0010.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9982311
X-RAY DIFFRACTIONr_angle_other_deg0.84133884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69624.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32415296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.465156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 32 -
Rwork0.185 784 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: -12.0207 Å / Origin y: -0.551 Å / Origin z: -13.4748 Å
111213212223313233
T0.0327 Å20.028 Å2-0.0126 Å2-0.117 Å2-0.0132 Å2--0.0344 Å2
L1.5621 °2-0.5979 °20.6503 °2-0.5587 °2-0.4173 °2--0.6023 °2
S0.1799 Å °0.0164 Å °-0.124 Å °-0.0514 Å °-0.0625 Å °0.0295 Å °0.0465 Å °0.0461 Å °-0.1174 Å °

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