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- PDB-3s0i: Crystal Structure of D48V mutant of Human Glycolipid Transfer Pro... -

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Basic information

Entry
Database: PDB / ID: 3s0i
TitleCrystal Structure of D48V mutant of Human Glycolipid Transfer Protein complexed with 3-O-sulfo galactosylceramide containing nervonoyl acyl chain
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / GLTP-fold / transport
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
Chem-CIS / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSamygina, V. / Popov, A.N. / Cabo-Bilbao, A. / Ochoa-Lizarralde, B. / Patel, D.J. / Brown, R.E. / Malinina, L.
CitationJournal: Structure / Year: 2011
Title: Enhanced selectivity for sulfatide by engineered human glycolipid transfer protein.
Authors: Samygina, V.R. / Popov, A.N. / Cabo-Bilbao, A. / Ochoa-Lizarralde, B. / Goni-de-Cerio, F. / Zhai, X. / Molotkovsky, J.G. / Patel, D.J. / Brown, R.E. / Malinina, L.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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)24,7522
Polymers23,8621
Non-polymers8901
Water3,027168
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5044
Polymers47,7242
Non-polymers1,7812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5630 Å2
ΔGint-42 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.315, 47.454, 63.257
Angle α, β, γ (deg.)90.00, 125.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycolipid transfer protein / / GLTP


Mass: 23861.820 Da / Num. of mol.: 1 / Mutation: D48V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2
#2: Chemical ChemComp-CIS / (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE / (2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL / CIS-TETRACOSENOYL SULFATIDE


Mass: 890.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H91NO11S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 273 K / pH: 7
Details: 20-25% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9754
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 30330 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RZN

3rzn


Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.82 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20599 1469 4.9 %RANDOM
Rwork0.15408 ---
obs0.15648 28748 99.53 %-
all-30330 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.09 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 61 168 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2942.0072358
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36424.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.73156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_nbd_refined0.240.2445
X-RAY DIFFRACTIONr_nbd_other0.1930.21306
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2888
X-RAY DIFFRACTIONr_nbtor_other0.0920.2830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1081.51336
X-RAY DIFFRACTIONr_mcbond_other0.8471.5403
X-RAY DIFFRACTIONr_mcangle_it2.43521669
X-RAY DIFFRACTIONr_scbond_it3.5023863
X-RAY DIFFRACTIONr_scangle_it4.4294.5702
X-RAY DIFFRACTIONr_rigid_bond_restr3.21131747
X-RAY DIFFRACTIONr_sphericity_free27.668544
X-RAY DIFFRACTIONr_sphericity_bonded16.51351832
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 91 -
Rwork0.25 2035 -
obs--98.43 %

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