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- PDB-9efn: Crystal structure of Saccharomyces cerevisiae cross-linked Sfh1 (... -

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Basic information

Entry
Database: PDB / ID: 9efn
TitleCrystal structure of Saccharomyces cerevisiae cross-linked Sfh1 (K197C, F233C) mutant in complex with phosphatidylethanolamine
ComponentsCRAL-TRIO domain-containing protein YKL091C
KeywordsLIPID BINDING PROTEIN / Sfh1 Sec14 homolog PITP / SIGNALING PROTEIN
Function / homology
Function and homology information


phosphatidylinositol transfer activity / post-Golgi vesicle-mediated transport / phosphatidylcholine binding / phosphatidylinositol binding / nucleus
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
PHOSPHATIDYLETHANOLAMINE / CRAL-TRIO domain-containing protein YKL091C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGreen, S.M. / Laganowsky, A. / Krieger, I. / Singh, P.K. / Sacchettini, J. / Igumenova, T.I. / Bankaitis, V.A.
Funding support United States, 4items
OrganizationGrant numberCountry
Welch FoundationA-2194-20240404 United States
Robert A. Welch FoundationBE-0017 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R35 GM131804 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH RO1 GM108998 United States
CitationJournal: To Be Published
Title: Crystal structure of Saccharomyces cerevisiae cross-linked Sfh1 (K197C, F233C) mutant in complex with phosphatidylethanolamine
Authors: Green, S.M. / Laganowsky, A. / Krieger, I. / Singh, P.K. / Sacchettini, J. / Igumenova, T.I. / Bankaitis, V.A.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRAL-TRIO domain-containing protein YKL091C
B: CRAL-TRIO domain-containing protein YKL091C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,40712
Polymers72,1792
Non-polymers2,22910
Water9,962553
1
A: CRAL-TRIO domain-containing protein YKL091C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2086
Polymers36,0891
Non-polymers1,1185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CRAL-TRIO domain-containing protein YKL091C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2006
Polymers36,0891
Non-polymers1,1105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.430, 72.010, 114.680
Angle α, β, γ (deg.)90.000, 93.950, 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 CRAL-TRIO domain-containing protein YKL091C


Mass: 36089.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKL091C / Production host: Escherichia coli (E. coli) / Strain (production host): phage resistant BL21-DE3 / References: UniProt: P33324
#2: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.75→49.31 Å / Num. obs: 80061 / % possible obs: 98.78 % / Redundancy: 4 % / Biso Wilson estimate: 20.73 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.142 / Net I/σ(I): 7.23
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 4.2 % / Num. unique obs: 7936 / CC1/2: 0.681 / Rrim(I) all: 0.99 / % possible all: 98.62

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.46 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.7689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 4003 5 %
Rwork0.2407 76029 -
obs0.2426 80032 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5063 0 142 554 5759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795393
X-RAY DIFFRACTIONf_angle_d0.96347288
X-RAY DIFFRACTIONf_chiral_restr0.0536765
X-RAY DIFFRACTIONf_plane_restr0.0094915
X-RAY DIFFRACTIONf_dihedral_angle_d11.8058787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.40261380.36542614X-RAY DIFFRACTION98.67
1.77-1.790.40341360.34342584X-RAY DIFFRACTION98.41
1.79-1.810.39881380.32572615X-RAY DIFFRACTION98.82
1.81-1.840.3451360.32672598X-RAY DIFFRACTION98.45
1.84-1.860.31271370.29682605X-RAY DIFFRACTION98.99
1.86-1.890.39381370.29462594X-RAY DIFFRACTION98.27
1.89-1.920.31671370.27562599X-RAY DIFFRACTION99.24
1.92-1.950.31651370.27532605X-RAY DIFFRACTION98.14
1.95-1.980.29111390.25822647X-RAY DIFFRACTION99.64
1.98-2.010.29151350.26062562X-RAY DIFFRACTION98.54
2.01-2.050.32771400.24952660X-RAY DIFFRACTION98.66
2.05-2.090.30421370.26042604X-RAY DIFFRACTION99.31
2.09-2.130.30141360.25832594X-RAY DIFFRACTION98.17
2.13-2.180.31061380.27192623X-RAY DIFFRACTION98.47
2.18-2.230.34571380.26452613X-RAY DIFFRACTION99.42
2.23-2.290.31721370.25752613X-RAY DIFFRACTION98.92
2.29-2.350.26561390.25692641X-RAY DIFFRACTION98.86
2.35-2.420.27561380.25852613X-RAY DIFFRACTION98.96
2.42-2.50.30341400.25522650X-RAY DIFFRACTION99.15
2.5-2.580.27681370.25972613X-RAY DIFFRACTION98.92
2.58-2.690.30571370.25972596X-RAY DIFFRACTION99.35
2.69-2.810.28861390.26112653X-RAY DIFFRACTION99.18
2.81-2.960.31111400.25772644X-RAY DIFFRACTION99.25
2.96-3.140.27071380.24992626X-RAY DIFFRACTION98.57
3.14-3.390.24751390.22032641X-RAY DIFFRACTION98.58
3.39-3.730.2261370.20242604X-RAY DIFFRACTION98.03
3.73-4.270.21971380.19122618X-RAY DIFFRACTION98.08
4.27-5.370.26421400.1952664X-RAY DIFFRACTION98.66
5.37-46.460.22661450.21262736X-RAY DIFFRACTION99.21
Refinement TLS params.Method: refined / Origin x: -1.26621834909 Å / Origin y: -20.3980313688 Å / Origin z: 28.5586656968 Å
111213212223313233
T0.141443606001 Å20.0014653263195 Å2-0.00500299050612 Å2-0.150271226685 Å2-0.00189086379843 Å2--0.199625057117 Å2
L-0.0106354699862 °2-0.0300845697893 °2-0.060285206922 °2-0.298460085555 °20.406418678187 °2--0.685834509391 °2
S-0.00626553715575 Å °-0.00110453796372 Å °0.0147526480523 Å °-0.00838346244942 Å °0.00998395294423 Å °0.000294147958205 Å °-0.0159322111361 Å °-0.0068672368271 Å °-0.0037474778705 Å °
Refinement TLS groupSelection details: all

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