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- PDB-3rzn: Crystal Structure of Human Glycolipid Transfer Protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 3rzn
TitleCrystal Structure 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 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
Chem-CIS / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSamygina, V. / Cabo-Bilbao, A. / Popov, A.N. / 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 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)24,7682
Polymers23,8781
Non-polymers8901
Water6,954386
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5364
Polymers47,7562
Non-polymers1,7812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5620 Å2
ΔGint-32 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.891, 50.060, 65.404
Angle α, β, γ (deg.)90.00, 118.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-491-

HOH

21A-583-

HOH

DetailsTHE BIOLOGICAL UNIT HAS BEEN VERIFIED BY DLS METHOD.

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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 / 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


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 273 K / pH: 5.1
Details: 20-25% PEG 8000, pH 5.1, 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: 0.9763
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 96462 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19
Reflection shellResolution: 1.1→1.15 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.67 / % possible all: 99.5

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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: 1SWX

1swx


Resolution: 1.1→14.97 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.672 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.157 4312 5 %RANDOM
Rwork0.138 ---
obs0.139 81298 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.2 Å2
2---0.27 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.1→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 61 386 2107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221810
X-RAY DIFFRACTIONr_bond_other_d0.0070.021277
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0012444
X-RAY DIFFRACTIONr_angle_other_deg1.88133159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6325.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99715330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.758156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_nbd_refined0.2310.2435
X-RAY DIFFRACTIONr_nbd_other0.1790.21345
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2908
X-RAY DIFFRACTIONr_nbtor_other0.0970.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0161.51374
X-RAY DIFFRACTIONr_mcbond_other0.8021.5411
X-RAY DIFFRACTIONr_mcangle_it2.30821704
X-RAY DIFFRACTIONr_scbond_it3.3183899
X-RAY DIFFRACTIONr_scangle_it4.2984.5738
X-RAY DIFFRACTIONr_rigid_bond_restr1.71333822
X-RAY DIFFRACTIONr_sphericity_free7.3853386
X-RAY DIFFRACTIONr_sphericity_bonded4.61633045
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 330 -
Rwork0.164 5948 -
obs--99.12 %

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