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- PDB-2evl: Crystal structure of human Glycolipid Transfer Protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 2evl
TitleCrystal structure of human Glycolipid Transfer Protein complexed with 18:2 Galactosylceramide
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / protein-glycolipid complex
Function / homology
Function and homology information


Glycosphingolipid biosynthesis / glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / glycosphingolipid metabolic process / intermembrane lipid transfer / response to immobilization stress ...Glycosphingolipid biosynthesis / glycolipid transfer activity / lipid transfer activity / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / glycolipid binding / glycosphingolipid metabolic process / 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
LINOLEIC ACID / beta-D-galactopyranose / PENTANE / N-OCTANE / SPHINGOSINE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalinina, L. / Malakhova, M.L. / Kanack, A.T. / Abagyan, R. / Brown, R.E. / Patel, D.J.
CitationJournal: Plos Biol. / Year: 2006
Title: The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure.
Authors: Malinina, L. / Malakhova, M.L. / Kanack, A.T. / Lu, M. / Abagyan, R. / Brown, R.E. / Patel, D.J.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)24,8246
Polymers23,8781
Non-polymers9465
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.705, 49.312, 68.481
Angle α, β, γ (deg.)90.00, 122.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycolipid transfer protein / / GLTP


Mass: 23877.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTP / Plasmid: PET30 XA-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 163 molecules

#3: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#4: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID / Linoleic acid


Mass: 280.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O2
#5: Chemical ChemComp-LNK / PENTANE / Pentane


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#6: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 15-20% PEG 3350 or 8000, 50 mM potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 15, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 10918 / Num. obs: 10918 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Χ2: 0.998 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.39 / Num. unique all: 1084 / Χ2: 0.953 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EUK

2euk


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.634 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 523 4.8 %RANDOM
Rwork0.183 ---
all0.186 10917 --
obs0.186 10917 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.776 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20.05 Å2
2--0.75 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 64 159 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221749
X-RAY DIFFRACTIONr_bond_other_d0.0010.021661
X-RAY DIFFRACTIONr_angle_refined_deg1.27422351
X-RAY DIFFRACTIONr_angle_other_deg0.88733870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52824.45974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11715297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.062157
X-RAY DIFFRACTIONr_chiral_restr0.070.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined0.20.2430
X-RAY DIFFRACTIONr_nbd_other0.170.21647
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2852
X-RAY DIFFRACTIONr_nbtor_other0.1130.2895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1260.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.212
X-RAY DIFFRACTIONr_mcbond_it0.8071.51127
X-RAY DIFFRACTIONr_mcbond_other0.1331.5409
X-RAY DIFFRACTIONr_mcangle_it1.18821660
X-RAY DIFFRACTIONr_scbond_it1.7013801
X-RAY DIFFRACTIONr_scangle_it2.5394.5691
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 46 -
Rwork0.203 754 -
obs-800 98.28 %

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