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- PDB-4omk: Crystal structure of SPF bound to squalene -

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Basic information

Entry
Database: PDB / ID: 4omk
TitleCrystal structure of SPF bound to squalene
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
ISOPROPYL ALCOHOL / Chem-SQL / SEC14-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

Downloads & links

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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)65,56714
Polymers63,9782
Non-polymers1,58912
Water15,367853
1
A: SEC14-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7847
Polymers31,9891
Non-polymers7946
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SEC14-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7847
Polymers31,9891
Non-polymers7946
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.270, 73.540, 94.230
Angle α, β, γ (deg.)90.00, 96.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 865 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SQL / (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene / squalene / Squalene


Mass: 410.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H50
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 3.83 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 97554 / Num. obs: 97261 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.6 / Num. unique all: 14143 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O6U

1o6u


Resolution: 1.75→29.887 Å / SU ML: 0.17 / σ(F): 1.19 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 4866 5.01 %RANDOM
Rwork0.1482 ---
obs0.1495 97261 93.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 100 853 5387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014753
X-RAY DIFFRACTIONf_angle_d1.7066422
X-RAY DIFFRACTIONf_dihedral_angle_d12.8171917
X-RAY DIFFRACTIONf_chiral_restr0.049668
X-RAY DIFFRACTIONf_plane_restr0.008827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.26573000.2495770X-RAY DIFFRACTION95
1.7699-1.79070.24982960.2295755X-RAY DIFFRACTION94
1.7907-1.81250.26073230.2245664X-RAY DIFFRACTION94
1.8125-1.83550.23522970.20945763X-RAY DIFFRACTION94
1.8355-1.85960.26452670.20885737X-RAY DIFFRACTION94
1.8596-1.88510.24272810.19865783X-RAY DIFFRACTION94
1.8851-1.9120.21493090.17985649X-RAY DIFFRACTION95
1.912-1.94060.20152830.17435687X-RAY DIFFRACTION93
1.9406-1.97090.19063100.1715737X-RAY DIFFRACTION94
1.9709-2.00320.20512720.16835677X-RAY DIFFRACTION94
2.0032-2.03770.19682930.1665662X-RAY DIFFRACTION93
2.0377-2.07480.19482850.15995642X-RAY DIFFRACTION93
2.0748-2.11470.20582920.1635484X-RAY DIFFRACTION90
2.1147-2.15780.1712400.14425325X-RAY DIFFRACTION87
2.1578-2.20470.16252690.14285247X-RAY DIFFRACTION87
2.2047-2.2560.17772790.13885500X-RAY DIFFRACTION91
2.256-2.31240.15343240.14035691X-RAY DIFFRACTION94
2.3124-2.37490.18083200.13925683X-RAY DIFFRACTION93
2.3749-2.44470.16563470.13615706X-RAY DIFFRACTION95
2.4447-2.52360.16643250.13425807X-RAY DIFFRACTION96
2.5236-2.61370.15083300.13095767X-RAY DIFFRACTION95
2.6137-2.71830.17173130.13955733X-RAY DIFFRACTION95
2.7183-2.8420.18782970.14045739X-RAY DIFFRACTION94
2.842-2.99170.182810.14365632X-RAY DIFFRACTION94
2.9917-3.17890.1633620.13315704X-RAY DIFFRACTION95
3.1789-3.4240.13433130.13465840X-RAY DIFFRACTION96
3.424-3.7680.15472660.13215692X-RAY DIFFRACTION94
3.768-4.31180.14452780.11995330X-RAY DIFFRACTION88
4.3118-5.42720.15333060.12716051X-RAY DIFFRACTION99
5.4272-29.8870.19473330.17916013X-RAY DIFFRACTION99

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