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- PDB-4kbs: Crystal structure of human ceramide-1-phosphate transfer protein ... -

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Basic information

Entry
Database: PDB / ID: 4kbs
TitleCrystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 12:0 phosphatidic acid (12:0 PA)
ComponentsGlycolipid transfer protein domain-containing protein 1
KeywordsLIPID TRANSPORT / Lipid transfer protein / GLTP-fold / CPTP / C1P / Ceramide-1-phosphate / Protein-lipid complex / Eicosanoid
Function / homology
Function and homology information


ceramide 1-phosphate transport / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy ...ceramide 1-phosphate transport / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy / phospholipid binding / endosome membrane / Golgi apparatus / plasma membrane / 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
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Ceramide-1-phosphate transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.898 Å
AuthorsSimanshu, D.K. / Brown, R.E. / Patel, D.J.
CitationJournal: Nature / Year: 2013
Title: Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids.
Authors: Simanshu, D.K. / Kamlekar, R.K. / Wijesinghe, D.S. / Zou, X. / Zhai, X. / Mishra, S.K. / Molotkovsky, J.G. / Malinina, L. / Hinchcliffe, E.H. / Chalfant, C.E. / Brown, R.E. / Patel, D.J.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Apr 3, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Glycolipid transfer protein domain-containing protein 1
B: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1646
Polymers48,9682
Non-polymers1,1954
Water4,936274
1
A: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0202
Polymers24,4841
Non-polymers5361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1444
Polymers24,4841
Non-polymers6603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.910, 78.116, 107.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycolipid transfer protein domain-containing protein 1


Mass: 24484.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTPD1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q5TA50
#2: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H52O8P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium acetate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31943 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.058 / Χ2: 1.153 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.90.45930920.828198.6
1.97-2.0560.29531460.8199.6
2.05-2.1460.20731560.924199.8
2.14-2.2560.14331520.96199.8
2.25-2.3960.10331860.991100
2.39-2.5860.08531721.0551100
2.58-2.8460.06831991.21199.8
2.84-3.255.80.05832181.714199.9
3.25-4.095.60.0532501.975199.6
4.09-505.50.03533721.125198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human ceramide-1-phosphate transfer protein in complex with 2:0 Ceramide-1-phosphate (2:0 C1P)

Resolution: 1.898→32.622 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1946 6.27 %Random
Rwork0.1884 ---
obs0.1913 31035 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.36 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 86.21 Å2 / Biso mean: 32.8411 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.7804 Å20 Å2-0 Å2
2---0.1928 Å2-0 Å2
3----1.5876 Å2
Refinement stepCycle: LAST / Resolution: 1.898→32.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 80 274 3638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053480
X-RAY DIFFRACTIONf_angle_d0.8714719
X-RAY DIFFRACTIONf_chiral_restr0.058534
X-RAY DIFFRACTIONf_plane_restr0.009596
X-RAY DIFFRACTIONf_dihedral_angle_d17.3171311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8977-1.94520.27751250.20671826195188
1.9452-1.99780.31111330.2131959209293
1.9978-2.05650.30741280.21471987211594
2.0565-2.12290.29061370.21182024216196
2.1229-2.19880.26391370.19592046218397
2.1988-2.28680.26791340.19442062219697
2.2868-2.39080.24941430.18982102224598
2.3908-2.51680.23441410.18752105224699
2.5168-2.67440.23741400.19362117225799
2.6744-2.88080.23451410.19142125226699
2.8808-3.17050.27341450.20682145229099
3.1705-3.62880.23961440.18442165230999
3.6288-4.56990.20891470.16221832330100
4.5699-32.62660.17351510.18252243239497

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