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- PDB-3s0k: Crystal Structure of Human Glycolipid Transfer Protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 3s0k
TitleCrystal Structure of Human Glycolipid Transfer Protein complexed with glucosylceramide containing oleoyl acyl chain (18:1)
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 1-phosphate binding / ceramide transport / 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 1-phosphate binding / ceramide transport / 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-03F / NICKEL (II) ION / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCabo-Bilbao, A. / Samygina, V. / Popov, A.N. / Ochoa-Lizarralde, B. / Goni-de-Cerio, F. / 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6633
Polymers23,8781
Non-polymers7852
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.659, 61.646, 67.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-03F / (9Z)-N-[(2S,3R,4E)-1-(beta-D-glucopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]octadec-9-enamide / N-(9Z-octadecenoyl)-1--glucosyl-sphing-4-enine


Mass: 726.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H79NO8
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 273 K / pH: 6.5
Details: 20-25% PEG 3350 , 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9756
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 41140 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.4→1.45 Å / % possible all: 90.4

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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 / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.143 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2096 5.1 %RANDOM
Rwork0.15 ---
obs0.152 39019 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 52 293 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221750
X-RAY DIFFRACTIONr_bond_other_d0.0020.021234
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9962360
X-RAY DIFFRACTIONr_angle_other_deg1.45333035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0775202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94524.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91215311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.853157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
X-RAY DIFFRACTIONr_nbd_refined0.2450.2446
X-RAY DIFFRACTIONr_nbd_other0.1830.21281
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2899
X-RAY DIFFRACTIONr_nbtor_other0.0910.2826
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.091.51333
X-RAY DIFFRACTIONr_mcbond_other0.741.5403
X-RAY DIFFRACTIONr_mcangle_it2.37221655
X-RAY DIFFRACTIONr_scbond_it3.5343860
X-RAY DIFFRACTIONr_scangle_it4.6124.5705
X-RAY DIFFRACTIONr_rigid_bond_restr2.18933713
X-RAY DIFFRACTIONr_sphericity_free8.3923295
X-RAY DIFFRACTIONr_sphericity_bonded4.14332943
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 125 -
Rwork0.217 2489 -
obs--86.16 %

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