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- PDB-7wwd: Crystal structure of Saccharomyces cerevisiae Sfh2 complexed with... -

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Basic information

Entry
Database: PDB / ID: 7wwd
TitleCrystal structure of Saccharomyces cerevisiae Sfh2 complexed with squalene
ComponentsPhosphatidylinositol transfer protein CSR1
KeywordsLIPID TRANSPORT / Sec14 / phosphatidylinositol / squalene / transport
Function / homology
Function and homology information


negative regulation of phosphatidylglycerol biosynthetic process / positive regulation of phosphatidylcholine biosynthetic process / phosphatidylinositol transfer activity / prospore membrane / phospholipid catabolic process / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / phospholipid transport ...negative regulation of phosphatidylglycerol biosynthetic process / positive regulation of phosphatidylcholine biosynthetic process / phosphatidylinositol transfer activity / prospore membrane / phospholipid catabolic process / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / phospholipid transport / lipid droplet / endosome / endoplasmic reticulum / mitochondrion / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Chem-SQL / Phosphatidylinositol transfer protein CSR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChen, L. / Tan, L. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1085530 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural basis of ligand recognition and transport by Sfh2, a yeast phosphatidylinositol transfer protein of the Sec14 superfamily.
Authors: Chen, L. / Tan, L. / Im, Y.J.
History
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol transfer protein CSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9812
Polymers46,5711
Non-polymers4111
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17070 Å2
Unit cell
Length a, b, c (Å)43.403, 78.278, 54.166
Angle α, β, γ (deg.)90.000, 94.113, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Phosphatidylinositol transfer protein CSR1 / CHS5 SPA2 rescue protein 1 / SEC14 homolog protein 2


Mass: 46570.641 Da / Num. of mol.: 1 / Mutation: deletion of loop residues (44-49 and 61-66)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: CSR1, SFH2, YLR380W / Plasmid: pHIS2-Thr
Details (production host): N-terminal thrombin cleavable hexahistidine-tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06705
#2: 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.: 1 / Source method: obtained synthetically / Formula: C30H50 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES pH7.0 0.1M KNO3, 30% PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 13881 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.05 / Net I/σ(I): 25.1
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 700 / CC1/2: 0.921 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→32.66 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4807 / Details: AlphaFold Q06705 was used as the starting model.
RfactorNum. reflection% reflection
Rfree0.2622 1388 10.03 %
Rwork0.1996 12449 -
obs0.2059 13837 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.09 Å2
Refinement stepCycle: LAST / Resolution: 2.39→32.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 30 88 3075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01463063
X-RAY DIFFRACTIONf_angle_d1.71894157
X-RAY DIFFRACTIONf_chiral_restr0.0957452
X-RAY DIFFRACTIONf_plane_restr0.0136528
X-RAY DIFFRACTIONf_dihedral_angle_d6.52681839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.480.29721330.22211207X-RAY DIFFRACTION94.04
2.48-2.580.3511490.23991285X-RAY DIFFRACTION99.93
2.58-2.70.33221390.24081272X-RAY DIFFRACTION100
2.7-2.840.30041410.24751261X-RAY DIFFRACTION99.79
2.84-3.010.30421470.23691288X-RAY DIFFRACTION99.93
3.01-3.250.32091440.24361292X-RAY DIFFRACTION99.93
3.25-3.570.2741420.2051273X-RAY DIFFRACTION99.02
3.57-4.090.22581060.1925960X-RAY DIFFRACTION74.13
4.09-5.150.19581430.1541292X-RAY DIFFRACTION99.72
5.15-32.660.21691440.15371319X-RAY DIFFRACTION99.32

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