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- PDB-1swx: Crystal structure of a human glycolipid transfer protein in apo-form -

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Basic information

Entry
Database: PDB / ID: 1swx
TitleCrystal structure of a human glycolipid transfer protein in apo-form
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / glycosphingolipid intermembrane transfer protein
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
HEXANE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsMalinina, L. / Malakhova, M.L. / Teplov, A. / Brown, R.E. / Patel, D.J.
CitationJournal: Nature / Year: 2004
Title: Structural basis for glycosphingolipid transfer specificity.
Authors: Malinina, L. / Malakhova, M.L. / Teplov, A. / Brown, R.E. / Patel, D.J.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)23,9642
Polymers23,8781
Non-polymers861
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.439, 35.259, 57.507
Angle α, β, γ (deg.)90.00, 115.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2
#2: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 3350, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
SYNCHROTRONAPS 19-BM2
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS HTC1IMAGE PLATEJun 25, 2003mirrors
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21
ReflectionResolution: 1.65→50 Å / Num. all: 23782 / Num. obs: 23776 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.34 / Num. unique all: 1051

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.205 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22567 1202 5.1 %RANDOM
Rwork0.17249 ---
all0.1753 23167 --
obs0.17536 22569 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.075 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å2-0.21 Å2
2---0.19 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 6 243 1854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221648
X-RAY DIFFRACTIONr_bond_other_d0.0020.021529
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9692227
X-RAY DIFFRACTIONr_angle_other_deg1.62733578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435196
X-RAY DIFFRACTIONr_chiral_restr0.0830.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
X-RAY DIFFRACTIONr_nbd_refined0.2450.2445
X-RAY DIFFRACTIONr_nbd_other0.2460.21784
X-RAY DIFFRACTIONr_nbtor_other0.1110.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0280.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.223
X-RAY DIFFRACTIONr_mcbond_it0.9031.5991
X-RAY DIFFRACTIONr_mcangle_it1.65321607
X-RAY DIFFRACTIONr_scbond_it2.7363657
X-RAY DIFFRACTIONr_scangle_it4.4684.5620
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 64
Rwork0.271 1480

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