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- PDB-4omj: Crystal structure of SPF bound to 2,3-oxidosqualene -

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Basic information

Entry
Database: PDB / ID: 4omj
TitleCrystal structure of SPF bound to 2,3-oxidosqualene
ComponentsSEC14-like protein 2
KeywordsTRANSPORT PROTEIN / cholesterol synthesis / squalene / 2 / 3-oxidosqualene / SEC14-like / CRAL-TRIO domain / hydrophobic ligand transporter
Function / homology
Function and homology information


vitamin E binding / regulation of cholesterol biosynthetic process / phospholipid binding / positive regulation of DNA-templated transcription / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / GOLD domain superfamily / GOLD domain / GOLD domain profile. / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain ...Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / GOLD domain superfamily / GOLD domain / GOLD domain profile. / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2TX / SEC14-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChristen, M. / Marcaida, M.J. / Lamprakis, C. / Cascella, M. / Stocker, A.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural insights on cholesterol endosynthesis: Binding of squalene and 2,3-oxidosqualene to supernatant protein factor.
Authors: Christen, M. / Marcaida, M.J. / Lamprakis, C. / Aeschimann, W. / Vaithilingam, J. / Schneider, P. / Hilbert, M. / Schneider, G. / Cascella, M. / Stocker, A.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Sep 20, 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: SEC14-like protein 2
B: SEC14-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,82320
Polymers63,9782
Non-polymers1,84518
Water19,1321062
1
A: SEC14-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,91711
Polymers31,9891
Non-polymers92810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SEC14-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9069
Polymers31,9891
Non-polymers9178
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 73.800, 94.450
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SEC14-like protein 2 / Alpha-tocopherol-associated protein / TAP / hTAP / Squalene transfer protein / Supernatant protein ...Alpha-tocopherol-associated protein / TAP / hTAP / Squalene transfer protein / Supernatant protein factor / SPF


Mass: 31989.086 Da / Num. of mol.: 2 / Fragment: UNP residues 1-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C22orf6, KIAA1186, KIAA1658, SEC14L2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 (DE3) / References: UniProt: O76054
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-2TX / (3S)-2,2-dimethyl-3-[(3E,7E,11E,15E)-3,7,12,16,20-pentamethylhenicosa-3,7,11,15,19-pentaen-1-yl]oxirane / 2,3-Oxidosqualene / 2,3-Oxidosqualene


Mass: 426.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H50O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1062 / 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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1 M Ammonium sulfate, 0.1 M Bis-Tris, 1% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.6→29.89 Å / Num. all: 129354 / Num. obs: 128890 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.2 / Num. unique all: 18675 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O6U

1o6u


Resolution: 1.6→29.89 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 17.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 6480 5.03 %random
Rwork0.1544 ---
obs0.1556 128780 99.58 %-
all-129354 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 106 1062 5592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014786
X-RAY DIFFRACTIONf_angle_d1.3366496
X-RAY DIFFRACTIONf_dihedral_angle_d12.3951926
X-RAY DIFFRACTIONf_chiral_restr0.076686
X-RAY DIFFRACTIONf_plane_restr0.008831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.27052070.21573950X-RAY DIFFRACTION99
1.6182-1.63720.24872110.21344124X-RAY DIFFRACTION99
1.6372-1.65720.23562190.20744000X-RAY DIFFRACTION99
1.6572-1.67820.21032020.19554068X-RAY DIFFRACTION100
1.6782-1.70020.20582060.1864070X-RAY DIFFRACTION100
1.7002-1.72350.23312080.1844095X-RAY DIFFRACTION100
1.7235-1.74820.19872140.17614074X-RAY DIFFRACTION100
1.7482-1.77420.19092010.17634082X-RAY DIFFRACTION100
1.7742-1.8020.19172050.17714068X-RAY DIFFRACTION100
1.802-1.83150.22022130.18844045X-RAY DIFFRACTION100
1.8315-1.86310.22662370.19464071X-RAY DIFFRACTION100
1.8631-1.8970.24172250.20234090X-RAY DIFFRACTION99
1.897-1.93340.19752450.17474040X-RAY DIFFRACTION100
1.9334-1.97290.21661990.16684075X-RAY DIFFRACTION100
1.9729-2.01580.20712200.16614065X-RAY DIFFRACTION100
2.0158-2.06270.19662090.15794100X-RAY DIFFRACTION100
2.0627-2.11420.19282190.15664049X-RAY DIFFRACTION100
2.1142-2.17140.17632090.15194057X-RAY DIFFRACTION99
2.1714-2.23530.19052030.15024034X-RAY DIFFRACTION98
2.2353-2.30740.17732410.15164039X-RAY DIFFRACTION99
2.3074-2.38980.16412270.14434060X-RAY DIFFRACTION100
2.3898-2.48540.17682340.14224075X-RAY DIFFRACTION100
2.4854-2.59850.17292310.14094059X-RAY DIFFRACTION100
2.5985-2.73540.17992080.14244127X-RAY DIFFRACTION100
2.7354-2.90670.16612230.14614069X-RAY DIFFRACTION100
2.9067-3.13090.16961960.15074142X-RAY DIFFRACTION100
3.1309-3.44550.16282300.14294084X-RAY DIFFRACTION99
3.4455-3.94310.15542210.13174111X-RAY DIFFRACTION100
3.9431-4.96420.13052030.12364147X-RAY DIFFRACTION100
4.9642-29.890.17932140.17634230X-RAY DIFFRACTION100

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