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- PDB-4ghp: Crystal Structure of D48V||A47D mutant of Human GLTP bound with 1... -

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Basic information

Entry
Database: PDB / ID: 4ghp
TitleCrystal Structure of D48V||A47D mutant of Human GLTP bound with 12:0 monosulfatide
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / GLTP-fold
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-EIS / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSamygina, V.R. / Ochoa-Lizarralde, B. / Popov, A.N. / 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
DepositionAug 8, 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 / 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)24,6302
Polymers23,9061
Non-polymers7241
Water91951
1
A: Glycolipid transfer protein
hetero molecules

A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2604
Polymers47,8122
Non-polymers1,4482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4570 Å2
ΔGint-17 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.331, 49.118, 68.120
Angle α, β, γ (deg.)90.00, 123.58, 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 / 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
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-20% PEG 3350, pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9754 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.82→15 Å / Num. all: 17073 / Num. obs: 16808 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.82→1.85 Å / % possible all: 96.2

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Processing

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

3ric


Resolution: 1.9→14.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.308 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.183 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24627 849 5.1 %RANDOM
Rwork0.21267 ---
all0.21447 15715 --
obs0.21447 15715 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.22 Å2
2--0.27 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 48 51 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221716
X-RAY DIFFRACTIONr_bond_other_d0.0010.021196
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9982320
X-RAY DIFFRACTIONr_angle_other_deg0.94632940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99224.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53715300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.718156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
X-RAY DIFFRACTIONr_nbd_refined0.2330.2452
X-RAY DIFFRACTIONr_nbd_other0.1920.21178
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2868
X-RAY DIFFRACTIONr_nbtor_other0.0910.2775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.280.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.29
X-RAY DIFFRACTIONr_mcbond_it1.2071.51315
X-RAY DIFFRACTIONr_mcbond_other0.2931.5403
X-RAY DIFFRACTIONr_mcangle_it1.39621649
X-RAY DIFFRACTIONr_scbond_it2.3553827
X-RAY DIFFRACTIONr_scangle_it3.3284.5671
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 63 -
Rwork0.243 1147 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: 11.1647 Å / Origin y: -0.3398 Å / Origin z: 14.492 Å
111213212223313233
T-0.0566 Å20.0064 Å20.0275 Å2--0.0837 Å2-0.039 Å2---0.1633 Å2
L3.2414 °21.283 °20.7588 °2-2.9414 °2-0.0506 °2--1.0392 °2
S0.2574 Å °0.0875 Å °-0.4218 Å °0.2742 Å °-0.0371 Å °0.0595 Å °0.0982 Å °-0.0685 Å °-0.2202 Å °

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