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- PDB-2bv7: Crystal structure of GLTP with bound GM3 -

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Basic information

Entry
Database: PDB / ID: 2bv7
TitleCrystal structure of GLTP with bound GM3
ComponentsGLYCOLIPID TRANSFER PROTEIN
KeywordsLIPID TRANSPORT / GLYCOLIPID / LIGAND BINDING / ACETYLATION / TRANSPORT / GLYCOLIPID TRANSFER PROTEIN
Function / homology
Function and homology information


lipid transfer activity / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / glycolipid binding / intermembrane lipid transfer / lipid 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-GM3 / Glycolipid transfer protein
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKidron, H. / Airenne, T.T. / Nymalm, Y. / Nylund, M. / West, G. / Mattjus, P. / Salminen, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structural Evidence for Adaptive Ligand Binding of Glycolipid Transfer Protein.
Authors: Airenne, T.T. / Kidron, H. / Nymalm, Y. / Nylund, M. / West, G. / Mattjus, P. / Salminen, T.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and X-Ray Analysis of Bovine Glycolipid Transfer Protein
Authors: West, G. / Nymalm, Y. / Airenne, T.T. / Kidron, H. / Mattjus, P. / Salminen, T.A.
History
DepositionJun 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)24,8544
Polymers23,8201
Non-polymers1,0343
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.500, 34.600, 58.300
Angle α, β, γ (deg.)90.00, 116.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCOLIPID TRANSFER PROTEIN / GLTP


Mass: 23819.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Organ: BRAIN / Plasmid: PQE9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P68265
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GM3 / N-{1-[(HEXOPYRANOSYLOXY)METHYL]-2-HYDROXYNONADECYL}TETRACOSANAMIDE


Mass: 842.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H99NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACCELERATES THE INTERMEMBRANE TRANSFER OF GLYCOLIPIDS

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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: 2.1 Å3/Da / Density % sol: 40.6 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 115280 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.14 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TFJ

1tfj


Resolution: 1.79→52.2 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.785 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 974 5.2 %RANDOM
Rwork0.189 ---
obs0.193 17930 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.58 Å2
2--0.04 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.79→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 54 119 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.35922338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66424.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21415302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.187159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2944
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21201
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9941.51044
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49321643
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1353780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3844.5695
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 72
Rwork0.223 1260

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