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- PDB-7wwe: Crystal structure of Saccharomyces cerevisiae Sfh2 in an apo form -

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Basic information

Entry
Database: PDB / ID: 7wwe
TitleCrystal structure of Saccharomyces cerevisiae Sfh2 in an apo form
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
Phosphatidylinositol transfer protein CSR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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


Theoretical massNumber of molelcules
Total (without water)46,5711
Polymers46,5711
Non-polymers00
Water3,477193
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 area17350 Å2
Unit cell
Length a, b, c (Å)42.920, 77.976, 53.628
Angle α, β, γ (deg.)90.000, 95.168, 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) / Strain (production host): BL21(DE3) / References: UniProt: Q06705
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES-NaOH pH 7, 0.1M KNO3, 30% PEG3350

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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: Aug 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17067 / % possible obs: 94.9 % / Redundancy: 4 % / Biso Wilson estimate: 19.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.027 / Net I/σ(I): 44.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Num. unique obs: 902 / CC1/2: 0.996 / Rpim(I) all: 0.033 / % possible all: 99.4

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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: 2.2→23.62 Å / SU ML: 0.2061 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3325 / Details: AlphaFold Q06705 was uased as the starting model.
RfactorNum. reflection% reflection
Rfree0.2575 1706 10.01 %
Rwork0.1962 15345 -
obs0.2024 17051 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 0 193 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793034
X-RAY DIFFRACTIONf_angle_d1.23484123
X-RAY DIFFRACTIONf_chiral_restr0.0543452
X-RAY DIFFRACTIONf_plane_restr0.0126528
X-RAY DIFFRACTIONf_dihedral_angle_d5.0191818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.28341460.21461312X-RAY DIFFRACTION96.81
2.26-2.340.26331460.20941313X-RAY DIFFRACTION99.18
2.34-2.420.28451480.20311338X-RAY DIFFRACTION99.53
2.42-2.520.26541490.20541339X-RAY DIFFRACTION99.53
2.52-2.630.32741500.21551346X-RAY DIFFRACTION99.53
2.63-2.770.26571460.21161321X-RAY DIFFRACTION99.46
2.77-2.940.26731500.20971337X-RAY DIFFRACTION99.66
2.94-3.170.27611490.20541346X-RAY DIFFRACTION99.2
3.17-3.490.25821460.19291313X-RAY DIFFRACTION97.72
3.49-3.990.22851390.17071248X-RAY DIFFRACTION92.41
3.99-5.020.19561230.17091114X-RAY DIFFRACTION82.14
5.02-100.26431140.19971018X-RAY DIFFRACTION73.51
Refinement TLS params.Method: refined / Origin x: 5.99474141224 Å / Origin y: -13.6307541482 Å / Origin z: 8.39188987011 Å
111213212223313233
T0.0867962121146 Å20.00455150647628 Å20.0101525280832 Å2-0.108911209699 Å20.019423278223 Å2--0.126137632768 Å2
L0.547531104883 °20.00353296176667 °20.110271426554 °2-0.641163359995 °20.147097899139 °2--1.23347067198 °2
S0.0438086881422 Å °-0.0183889748581 Å °-0.0696377060676 Å °0.0210676031664 Å °0.0202300935572 Å °-0.106723494672 Å °0.0350011533473 Å °0.111499823483 Å °-0.0470039374122 Å °
Refinement TLS groupSelection details: all

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