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- PDB-1wbe: X-ray structure of bovine GLTP -

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Basic information

Entry
Database: PDB / ID: 1wbe
TitleX-ray structure of bovine GLTP
ComponentsGLYCOLIPID TRANSFER PROTEIN
KeywordsLIPID TRANSPORT / GLYCOLIPID TRANSFER PROTEIN / GLYCOLIPID TRANSFER / ACETYLATION
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 / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsAirenne, T.T. / Kidron, H. / West, G. / Nymalm, Y. / Nylund, M. / 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
DepositionNov 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 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)24,2153
Polymers23,9511
Non-polymers2642
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.741, 35.393, 58.423
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCOLIPID TRANSFER PROTEIN / GLTP


Mass: 23950.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P68265
#2: Chemical ChemComp-DKA / DECANOIC ACID


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


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


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN ACCELERATES THE INTERMEMBRANE TRANSFER OF VARIOUS 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: 2.15 Å3/Da / Density % sol: 42.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.804
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.804 Å / Relative weight: 1
ReflectionResolution: 1.36→25 Å / Num. obs: 41883 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22
Reflection shellResolution: 1.36→1.45 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 73.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
ARP/wARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TFJ

1tfj


Resolution: 1.36→24.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.101 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2124 5.1 %RANDOM
Rwork0.184 ---
obs0.186 39758 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.12 Å2
2---0.02 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.36→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 18 292 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221835
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9812493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0915207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91424.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50115358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.594159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021336
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21018
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21284
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2561.51104
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83321768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.753848
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it44.5725
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: 1.36→1.4 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 113
Rwork0.292 2005

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