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- PDB-2evt: Crystal structure of D48V mutant of human Glycolipid Transfer Protein -

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Basic information

Entry
Database: PDB / ID: 2evt
TitleCrystal structure of D48V mutant of human Glycolipid Transfer Protein
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / D48V mutant human GLTP
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
HEXANE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMalinina, L. / Malakhova, M.L. / Teplov, A. / Brown, R.E. / Patel, D.J.
CitationJournal: Plos Biol. / Year: 2006
Title: The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure.
Authors: Malinina, L. / Malakhova, M.L. / Kanack, A.T. / Lu, M. / Abagyan, R. / Brown, R.E. / Patel, D.J.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 26, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN UNK ATOMS ARE UNKNOWN FRAGMENT OF HYDROCARBOM

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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)23,9482
Polymers23,8621
Non-polymers861
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.459, 35.360, 58.011
Angle α, β, γ (deg.)90.00, 116.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycolipid transfer protein / / GLTP


Mass: 23861.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30 XA-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2
#2: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 20, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. all: 13588 / Num. obs: 13588 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.104 / Χ2: 1.159 / Net I/σ(I): 18.7
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.498 / Num. unique all: 1298 / Χ2: 1.445 / % possible all: 94.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWX

1swx


Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.347 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 678 5 %RANDOM
Rwork0.201 ---
all0.203 13588 --
obs0.203 13587 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.389 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.33 Å2
2---1.21 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 6 222 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221669
X-RAY DIFFRACTIONr_bond_other_d0.0020.021549
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9672256
X-RAY DIFFRACTIONr_angle_other_deg1.17133621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585199
X-RAY DIFFRACTIONr_chiral_restr0.0560.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021794
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
X-RAY DIFFRACTIONr_nbd_refined0.1910.2453
X-RAY DIFFRACTIONr_nbd_other0.220.21749
X-RAY DIFFRACTIONr_nbtor_other0.0980.2943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.223
X-RAY DIFFRACTIONr_mcbond_it0.5341.51007
X-RAY DIFFRACTIONr_mcangle_it1.04121631
X-RAY DIFFRACTIONr_scbond_it1.4873662
X-RAY DIFFRACTIONr_scangle_it2.5944.5625
LS refinement shellResolution: 1.99→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.445 37
Rwork0.292 786
obs-823

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