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- PDB-3spw: Structure of Osh4p/Kes1p in complex with phosphatidylinositol 4-p... -

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Basic information

Entry
Database: PDB / ID: 3spw
TitleStructure of Osh4p/Kes1p in complex with phosphatidylinositol 4-phosphate
ComponentsProtein KES1
KeywordsPROTEIN BINDING / Lipid binding protein
Function / homology
Function and homology information


Acyl chain remodelling of PS / Synthesis of bile acids and bile salts / sterol transfer activity / ER to Golgi ceramide transport / sterol transport / post-Golgi vesicle-mediated transport / maintenance of cell polarity / sphingolipid metabolic process / phosphatidic acid binding / piecemeal microautophagy of the nucleus ...Acyl chain remodelling of PS / Synthesis of bile acids and bile salts / sterol transfer activity / ER to Golgi ceramide transport / sterol transport / post-Golgi vesicle-mediated transport / maintenance of cell polarity / sphingolipid metabolic process / phosphatidic acid binding / piecemeal microautophagy of the nucleus / oxysterol binding / phosphatidylinositol-4-phosphate binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / endocytosis / Golgi membrane / lipid binding / membrane / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #1150 / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Chem-T7M / Oxysterol-binding protein homolog 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDelfosse, V. / de Saint-Jean, M. / Douguet, D. / Antonny, B. / Drin, G. / Bourguet, W.
CitationJournal: J.Cell Biol. / Year: 2011
Title: Osh4p exchanges sterols for phosphatidylinositol 4-phosphate between lipid bilayers.
Authors: de Saint-Jean, M. / Delfosse, V. / Douguet, D. / Chicanne, G. / Payrastre, B. / Bourguet, W. / Antonny, B. / Drin, G.
History
DepositionJul 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein KES1
B: Protein KES1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3104
Polymers99,4042
Non-polymers1,9062
Water4,342241
1
A: Protein KES1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6552
Polymers49,7021
Non-polymers9531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein KES1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6552
Polymers49,7021
Non-polymers9531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.460, 54.760, 121.860
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein KES1 / Oxysterol-binding protein homolog 4


Mass: 49702.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: KES1, LPI3C, OSH4, P2614, YPL145C / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P35844
#2: Chemical ChemComp-T7M / (2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol-4-phosphate


Mass: 953.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H82O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 250 mM CaCl2, 100 mM MES, 16% PEG 20K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.6→47.29 Å / Num. all: 30180 / Num. obs: 30180 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.27 Å2 / Rsym value: 0.146 / Net I/σ(I): 6.82
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.78 / Num. unique all: 4633 / Rsym value: 0.49 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZHW

1zhw


Resolution: 2.6→47.29 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 1508 5 %RANDOM
Rwork0.2282 ---
obs0.2302 30173 99.8 %-
all-30173 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.601 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2188 Å2-0 Å27.9941 Å2
2---7.5176 Å2-0 Å2
3---9.7364 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6077 0 92 241 6410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026321
X-RAY DIFFRACTIONf_angle_d0.5968583
X-RAY DIFFRACTIONf_dihedral_angle_d12.5972275
X-RAY DIFFRACTIONf_chiral_restr0.04949
X-RAY DIFFRACTIONf_plane_restr0.0021100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.5999-2.68380.31931340.289925502550
2.6838-2.77970.32051370.28526122612
2.7797-2.89090.31491340.279725612561
2.8909-3.02250.30751360.264325882588
3.0225-3.18180.31771370.246625892589
3.1818-3.38110.30121370.235726122612
3.3811-3.64210.25521380.229326152615
3.6421-4.00840.28161360.209525852585
4.0084-4.5880.22251380.187126272627
4.588-5.77880.25351380.201926172617
5.7788-47.30560.2291430.225427092709

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