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

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Basic information

Entry
Database: PDB / ID: 7wvt
TitleCrystal structure of Saccharomyces cerevisiae Sfh2 complexed with phosphatidylinositol
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 / phosphatidylinositol metabolic process / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / phospholipid transport / Golgi to plasma membrane protein transport / phospholipid catabolic process ...negative regulation of phosphatidylglycerol biosynthetic process / positive regulation of phosphatidylcholine biosynthetic process / phosphatidylinositol transfer activity / prospore membrane / phosphatidylinositol metabolic process / negative regulation of fatty acid biosynthetic process / Golgi to plasma membrane transport / phospholipid transport / Golgi to plasma membrane protein transport / phospholipid catabolic process / 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-B7N / Phosphatidylinositol transfer protein CSR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 11, 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)47,4362
Polymers46,5711
Non-polymers8651
Water10,953608
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 area17060 Å2
Unit cell
Length a, b, c (Å)74.541, 117.132, 42.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
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-B7N / (1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate


Mass: 865.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H85O13P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.19 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 30% PEG 1000

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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: 1.5→50 Å / Num. obs: 59663 / % possible obs: 98 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Net I/σ(I): 40.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 2577 / CC1/2: 0.898 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.77 Å / SU ML: 0.1423 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: AlphaFold model Q06705 was used as the starting model.
RfactorNum. reflection% reflection
Rfree0.2115 2000 3.36 %
Rwork0.1687 57576 -
obs0.1702 59576 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 57 608 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643157
X-RAY DIFFRACTIONf_angle_d0.96674280
X-RAY DIFFRACTIONf_chiral_restr0.0806466
X-RAY DIFFRACTIONf_plane_restr0.007542
X-RAY DIFFRACTIONf_dihedral_angle_d25.13211182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.25781250.18833589X-RAY DIFFRACTION86.69
1.53-1.580.21761380.17073990X-RAY DIFFRACTION95.67
1.58-1.620.21961430.16274111X-RAY DIFFRACTION99.84
1.62-1.680.20071430.16054136X-RAY DIFFRACTION99.95
1.68-1.740.20161450.16164161X-RAY DIFFRACTION100
1.74-1.80.22571450.16914155X-RAY DIFFRACTION99.93
1.8-1.890.24331440.1744159X-RAY DIFFRACTION99.95
1.89-1.990.20811450.16784176X-RAY DIFFRACTION99.95
1.99-2.110.21321450.16224186X-RAY DIFFRACTION99.95
2.11-2.270.21460.15614188X-RAY DIFFRACTION99.91
2.27-2.50.1881460.16494217X-RAY DIFFRACTION99.89
2.5-2.860.20951470.1734229X-RAY DIFFRACTION99.86
2.86-3.610.20451480.1674248X-RAY DIFFRACTION99.32
3.61-28.770.22281400.1794031X-RAY DIFFRACTION90.13

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