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- PDB-4h2z: Crystal structure of human GLTP bound with 12:0 monosulfatide -

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Basic information

Entry
Database: PDB / ID: 4h2z
TitleCrystal structure of human GLTP bound with 12:0 monosulfatide
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-EIS / PENTADECANE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSamygina, V.R. / Ochoa-Lizarralde, B. / Malinina, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insights into lipid-dependent reversible dimerization of human GLTP.
Authors: Samygina, V.R. / Ochoa-Lizarralde, B. / Popov, A.N. / Cabo-Bilbao, A. / Goni-de-Cerio, F. / Molotkovsky, J.G. / Patel, D.J. / Brown, R.E. / Malinina, L.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0505
Polymers23,8781
Non-polymers1,1724
Water4,540252
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,09910
Polymers47,7562
Non-polymers2,3448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3330 Å2
ΔGint-15 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.605, 49.998, 65.457
Angle α, β, γ (deg.)90.00, 118.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-642-

HOH

31A-647-

HOH

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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-EIS / N-{(2S,3R,4E)-3-hydroxy-1-[(3-O-sulfo-beta-D-galactopyranosyl)oxy]octadec-4-en-2-yl}dodecanamide


Mass: 723.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H69NO11S
#3: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-20% pEG 3350, 0.1M MES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 39587 / Num. obs: 38717 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.45→1.48 Å / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RZN

3rzn


Resolution: 1.45→14.97 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.073 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.082 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19971 1859 5 %RANDOM
Rwork0.16013 ---
all0.16212 37205 --
obs0.16212 35346 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.36 Å2
2--0.48 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 72 252 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021824
X-RAY DIFFRACTIONr_bond_other_d0.0010.021849
X-RAY DIFFRACTIONr_angle_refined_deg1.9242.0042460
X-RAY DIFFRACTIONr_angle_other_deg0.88934295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9255210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72124.93881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.343157
X-RAY DIFFRACTIONr_chiral_restr0.1140.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.07433671
X-RAY DIFFRACTIONr_sphericity_free26.501562
X-RAY DIFFRACTIONr_sphericity_bonded11.28653829
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.601 145 -
Rwork0.571 2490 -
obs--96.91 %
Refinement TLS params.Method: refined / Origin x: 12.997 Å / Origin y: -0.253 Å / Origin z: 13.899 Å
111213212223313233
T0.0133 Å2-0.0005 Å20.0082 Å2-0.0143 Å20.0131 Å2--0.0247 Å2
L0.9985 °20.4511 °20.1726 °2-1.4329 °2-0.2027 °2--0.7616 °2
S0.0501 Å °-0.098 Å °-0.0625 Å °0.1258 Å °0.0237 Å °0.0923 Å °0.0124 Å °-0.0553 Å °-0.0738 Å °

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