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

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Basic information

Entry
Database: PDB / ID: 4gvt
TitleCrystal structure of D48V mutant of human GLTP bound with 12:0 disulfatide (hexagonal form)
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionAug 31, 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)24,6662
Polymers23,8621
Non-polymers8041
Water00
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2230 Å2
ΔGint-20 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.019, 111.019, 75.206
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-20% PEG 3350, pH 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: Apr 13, 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: 2.9→50 Å / Num. all: 6872 / Num. obs: 6872 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3.02 Å / % possible all: 95.6

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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: 4H2Z

4h2z


Resolution: 2.9→14.81 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.906 / SU B: 41.691 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28201 297 4.8 %RANDOM
Rwork0.19322 ---
all0.19771 6182 --
obs0.19771 5877 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 53 0 1712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221752
X-RAY DIFFRACTIONr_bond_other_d0.0040.021215
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.0012371
X-RAY DIFFRACTIONr_angle_other_deg0.95632987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9725205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34724.7374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08815304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.645156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.2480.2490
X-RAY DIFFRACTIONr_nbd_other0.1920.21277
X-RAY DIFFRACTIONr_nbtor_refined0.2040.2876
X-RAY DIFFRACTIONr_nbtor_other0.0930.2886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.23
X-RAY DIFFRACTIONr_mcbond_it0.8491.51323
X-RAY DIFFRACTIONr_mcbond_other0.0941.5409
X-RAY DIFFRACTIONr_mcangle_it1.01121672
X-RAY DIFFRACTIONr_scbond_it1.4633851
X-RAY DIFFRACTIONr_scangle_it2.3584.5699
LS refinement shellResolution: 2.901→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.496 17 -
Rwork0.378 408 -
obs--95.08 %

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