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- PDB-1tfj: Crystal structure of Bovine Glycolipid transfer protein in comple... -

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Basic information

Entry
Database: PDB / ID: 1tfj
TitleCrystal structure of Bovine Glycolipid transfer protein in complex with a fatty acid
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / Glycolipid
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
DECANOIC ACID / Glycolipid transfer protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.61 Å
AuthorsAirenne, T.T. / Kidron, H. / West, G. / Nymalm, Y. / 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.T.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)25,3944
Polymers25,0941
Non-polymers3003
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.395, 34.904, 58.168
Angle α, β, γ (deg.)90.00, 116.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycolipid transfer protein / GLTP


Mass: 25093.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GLTP / Plasmid: pQE-9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68265
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 8000, MES, Sodium acetate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.804 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2003 / Details: mirrors
RadiationMonochromator: triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.804 Å / Relative weight: 1
ReflectionResolution: 1.61→20 Å / Num. all: 26281 / Num. obs: 25509 / % possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.16
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.27 / Num. unique all: 3717 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MAR345data collection
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.61→18.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.955 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22141 1276 5 %RANDOM
Rwork0.18209 ---
all0.18405 24231 --
obs0.18405 24231 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20.42 Å2
2---0.28 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.61→18.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 19 151 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221756
X-RAY DIFFRACTIONr_bond_other_d0.0050.021640
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.962374
X-RAY DIFFRACTIONr_angle_other_deg0.87633838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85724.17779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09115326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.297159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined0.2330.2468
X-RAY DIFFRACTIONr_nbd_other0.1960.21679
X-RAY DIFFRACTIONr_nbtor_refined0.1970.2898
X-RAY DIFFRACTIONr_nbtor_other0.090.2885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.214
X-RAY DIFFRACTIONr_mcbond_it1.6671.51070
X-RAY DIFFRACTIONr_mcbond_other0.3061.5408
X-RAY DIFFRACTIONr_mcangle_it1.821682
X-RAY DIFFRACTIONr_scbond_it3.0163801
X-RAY DIFFRACTIONr_scangle_it4.2724.5692
LS refinement shellResolution: 1.61→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 --
Rwork0.242 1688 -
obs-3717 92.12 %

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