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- PDB-3ric: Crystal Structure of D48V||A47D mutant of Human Glycolipid Transf... -

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Basic information

Entry
Database: PDB / ID: 3ric
TitleCrystal Structure of D48V||A47D mutant of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1)
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / GLTP fold
Function / homology
Function and homology information


glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid transport / glycolipid binding / intermembrane lipid transfer / response to immobilization stress ...glycolipid transfer activity / lipid transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / Glycosphingolipid transport / glycolipid binding / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSamygina, V. / 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
DepositionApr 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Data collection
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)24,7962
Polymers23,9061
Non-polymers8901
Water1,13563
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5924
Polymers47,8122
Non-polymers1,7812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area5580 Å2
ΔGint-36 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.871, 48.128, 69.086
Angle α, β, γ (deg.)90.00, 123.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycolipid transfer protein / GLTP


Mass: 23905.830 Da / Num. of mol.: 1 / Fragment: Human Glycolipid Transfer Protein / Mutation: D48V, A47D
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, DNA-directed DNA polymerase
#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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 273 K / pH: 5.1
Details: 15-20% PEG 3350, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 11907 / % possible obs: 96 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.55 / % possible all: 93.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→14.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.717 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21881 570 4.8 %RANDOM
Rwork0.18191 ---
obs0.18378 11300 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.14 Å2
2--0.23 Å20 Å2
3---0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.195 Å0.288 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 61 63 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221781
X-RAY DIFFRACTIONr_bond_other_d0.0010.021257
X-RAY DIFFRACTIONr_angle_refined_deg1.6582.0042403
X-RAY DIFFRACTIONr_angle_other_deg0.96233090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38924.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18215313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.258157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.2150.2445
X-RAY DIFFRACTIONr_nbd_other0.1870.21238
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2865
X-RAY DIFFRACTIONr_nbtor_other0.0890.2860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9671.51352
X-RAY DIFFRACTIONr_mcbond_other0.2141.5411
X-RAY DIFFRACTIONr_mcangle_it1.18621685
X-RAY DIFFRACTIONr_scbond_it2.0313875
X-RAY DIFFRACTIONr_scangle_it2.8494.5718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 41 -
Rwork0.257 812 -
obs--93.84 %
Refinement TLS params.Method: refined / Origin x: -10.7349 Å / Origin y: -0.8487 Å / Origin z: -14.9749 Å
111213212223313233
T-0.0834 Å20.0077 Å20.0053 Å2--0.1527 Å20.0672 Å2---0.1791 Å2
L3.6979 °2-1.1342 °20.9295 °2-2.8786 °20.4038 °2--1.6891 °2
S0.1456 Å °-0.2158 Å °-0.276 Å °-0.2829 Å °0.0401 Å °-0.09 Å °-0.0146 Å °0.0287 Å °-0.1857 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 463
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A3 - 209

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