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- PDB-2evs: Crystal structure of human Glycolipid Transfer Protein complexed ... -

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Basic information

Entry
Database: PDB / ID: 2evs
TitleCrystal structure of human Glycolipid Transfer Protein complexed with n-hexyl-beta-D-glucoside
ComponentsGlycolipid transfer protein
KeywordsLIPID TRANSPORT / Protein complex with detergent
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
DECANE / alpha-D-glucopyranose / HEXANE / Glycolipid transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalinina, L. / Malakhova, M.L. / Kanack, A.T. / Abagyan, R. / 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 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycolipid transfer protein
E: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5178
Polymers47,7562
Non-polymers7616
Water4,846269
1
A: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3735
Polymers23,8781
Non-polymers4954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glycolipid transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1443
Polymers23,8781
Non-polymers2662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.913, 42.180, 70.819
Angle α, β, γ (deg.)90.00, 104.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

#1: Protein Glycolipid transfer protein / GLTP


Mass: 23877.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTP / Plasmid: PET30 XA-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD2
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 15-20% PEG 3350, potassium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 30, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 22940 / Num. obs: 22940 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Χ2: 1.039 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.452 / Num. unique all: 2236 / Χ2: 1.112 / % possible all: 98.1

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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: 2.2→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.363 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1179 5.1 %RANDOM
Rwork0.19 ---
all0.192 22916 --
obs0.192 22916 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.736 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0.6 Å2
2---0.48 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 52 269 3487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223301
X-RAY DIFFRACTIONr_bond_other_d0.0010.023065
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.984457
X-RAY DIFFRACTIONr_angle_other_deg1.47937155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84524.615143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63415584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5711512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
X-RAY DIFFRACTIONr_nbd_refined0.2220.2835
X-RAY DIFFRACTIONr_nbd_other0.1820.23095
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21622
X-RAY DIFFRACTIONr_nbtor_other0.0930.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.248
X-RAY DIFFRACTIONr_mcbond_it0.821.52187
X-RAY DIFFRACTIONr_mcbond_other0.1671.5787
X-RAY DIFFRACTIONr_mcangle_it1.13623184
X-RAY DIFFRACTIONr_scbond_it1.6931482
X-RAY DIFFRACTIONr_scangle_it2.4954.51273
LS refinement shellResolution: 2.2→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 86 -
Rwork0.212 1438 -
obs-1524 91.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9571-0.0376-0.28540.94150.20881.87020.03460.0922-0.0899-0.08620.00030.0831-0.022-0.1102-0.0349-0.1159-0.00480.0088-0.18620.0096-0.124670.3390.244811.3047
21.556-0.0189-0.00483.3916-1.03762.69360.0171-0.4213-0.00970.16050.1630.5251-0.1629-0.601-0.18020.00470.0266-0.04680.43850.02110.185445.0489-10.244520.1883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 209
2X-RAY DIFFRACTION1A300 - 301
3X-RAY DIFFRACTION1A302
4X-RAY DIFFRACTION2E18 - 209
5X-RAY DIFFRACTION2E310 - 312

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