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- PDB-6w32: Crystal structure of Sfh5 -

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Basic information

Entry
Database: PDB / ID: 6w32
TitleCrystal structure of Sfh5
ComponentsPhosphatidylinositol transfer protein SFH5
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


phosphatidylinositol transfer activity / endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
Phosphatidylinositol transfer protein Sfh5 / 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
PROTOPORPHYRIN IX CONTAINING FE / Phosphatidylinositol transfer protein SFH5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsGulten, G. / Khan, D. / Aggarwal, A. / Krieger, I. / Sacchettini, J.C. / Bankaitis, V.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Elife / Year: 2020
Title: A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins.
Authors: Khan, D. / Lee, D. / Gulten, G. / Aggarwal, A. / Wofford, J. / Krieger, I. / Tripathi, A. / Patrick, J.W. / Eckert, D.M. / Laganowsky, A. / Sacchettini, J. / Lindahl, P. / Bankaitis, V.A.
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Phosphatidylinositol transfer protein SFH5
A: Phosphatidylinositol transfer protein SFH5
C: Phosphatidylinositol transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0336
Polymers107,1833
Non-polymers1,8493
Water00
1
B: Phosphatidylinositol transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3442
Polymers35,7281
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Phosphatidylinositol transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3442
Polymers35,7281
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphatidylinositol transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3442
Polymers35,7281
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)205.343, 205.343, 68.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphatidylinositol transfer protein SFH5 / PITP SFH5 / SEC14 homolog 5


Mass: 35727.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: YJM789 / Gene: SFH5, SCY_3146 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZQI5
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has ligand of interestN

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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: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M KSCN, 0.1 M Na-citrate (pH 4.2), 24% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.9→29.33 Å / Num. obs: 32843 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.064 / Rrim(I) all: 0.17 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.0672.2243323147300.5050.8812.3961.2100
9.17-29.336.10.051681911130.9970.0220.05533.494.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
XDSdata reduction
Aimless0.7.4data scaling
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.324 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 33.61
RfactorNum. reflection% reflection
Rfree0.3019 3091 5.03 %
Rwork0.2294 --
obs0.233 29752 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.83 Å2 / Biso mean: 81.4977 Å2 / Biso min: 30.8 Å2
Refinement stepCycle: final / Resolution: 2.9→29.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7040 0 129 0 7169
Biso mean--58.5 --
Num. residues----852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-2.94540.35721450.34162664100
2.9454-2.99360.40731640.34382659100
2.9936-3.04520.39711380.35082673100
3.0452-3.10050.38471370.33952644100
3.1005-3.16010.33361490.31492656100
3.1601-3.22450.39161490.31022641100
3.2245-3.29450.40521400.2982651100
3.2945-3.37110.32211540.28482657100
3.3711-3.45530.31221400.2852651100
3.4553-3.54850.3791260.2742689100
3.5485-3.65280.30941760.2647258999
3.6528-3.77040.29261520.23972682100
3.7704-3.90490.32141350.23242623100
3.9049-4.06080.31691630.23492658100
4.0608-4.24510.27181320.21852696100
4.2451-4.46820.311590.2037259699
4.4682-4.74710.3128940.19552706100
4.7471-5.11180.31191110.2032266699
5.1118-5.6230.29271530.2044265899
5.623-6.42920.28671130.2215266299
6.4292-8.0720.22281090.1944266399
8.072-29.3240.23571520.1683260298

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