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- PDB-3nsu: A Systematic Screen for Protein-Lipid Interactions in Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 3nsu
TitleA Systematic Screen for Protein-Lipid Interactions in Saccharomyces cerevisiae
ComponentsPhosphatidylinositol 4,5-bisphosphate-binding protein SLM1
KeywordsSIGNALING PROTEIN / Pleckstrin homology domain
Function / homology
Function and homology information


eisosome assembly / sphingolipid binding / establishment or maintenance of actin cytoskeleton polarity / endosomal transport / actin filament bundle assembly / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / protein localization to plasma membrane / regulation of cell growth / actin cytoskeleton organization ...eisosome assembly / sphingolipid binding / establishment or maintenance of actin cytoskeleton polarity / endosomal transport / actin filament bundle assembly / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / protein localization to plasma membrane / regulation of cell growth / actin cytoskeleton organization / mitochondrion / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Slm1, PH domain / SLM1/RGC1-like, BAR-like domain / SLM1/RGC1-like, PH domain / PH domain / BAR-like domain / AH/BAR domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Slm1, PH domain / SLM1/RGC1-like, BAR-like domain / SLM1/RGC1-like, PH domain / PH domain / BAR-like domain / AH/BAR domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGallego, O. / Fernandez-Tornero, C. / Aguilar-Gurrieri, C. / Muller, C. / Gavin, A.C.
CitationJournal: Mol. Syst. Biol. / Year: 2010
Title: A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Authors: Gallego, O. / Betts, M.J. / Gvozdenovic-Jeremic, J. / Maeda, K. / Matetzki, C. / Aguilar-Gurrieri, C. / Beltran-Alvarez, P. / Bonn, S. / Fernandez-Tornero, C. / Jensen, L.J. / Kuhn, M. / ...Authors: Gallego, O. / Betts, M.J. / Gvozdenovic-Jeremic, J. / Maeda, K. / Matetzki, C. / Aguilar-Gurrieri, C. / Beltran-Alvarez, P. / Bonn, S. / Fernandez-Tornero, C. / Jensen, L.J. / Kuhn, M. / Trott, J. / Rybin, V. / Muller, C.W. / Bork, P. / Kaksonen, M. / Russell, R.B. / Gavin, A.C.
History
DepositionJul 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
B: Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9396
Polymers27,5552
Non-polymers3844
Water1,928107
1
A: Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0664
Polymers13,7781
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8742
Polymers13,7781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.390, 73.050, 37.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1 / TORC2 effector protein SLM1 / Synthetic lethal with MSS4 protein 1


Mass: 13777.617 Da / Num. of mol.: 2 / Fragment: Pleckstrin Homology domain (unp residues 469-583)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIT2, SLM1, YIL105C / Plasmid: pET100-D/Topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40485
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M (NH4)2SO4, 2 % PEG 400, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15561 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.37 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 17.56
Reflection shellResolution: 2→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1136 / Rsym value: 0.642 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BTK

1btk


Resolution: 2→19.824 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 777 5 %Random
Rwork0.2213 ---
obs0.2239 15539 97.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.146 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 30.226 Å2
Baniso -1Baniso -2Baniso -3
1--6.1424 Å20 Å20 Å2
2--4.719 Å20 Å2
3---1.4233 Å2
Refinement stepCycle: LAST / Resolution: 2→19.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 20 107 1851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071782
X-RAY DIFFRACTIONf_angle_d1.0612394
X-RAY DIFFRACTIONf_dihedral_angle_d16.857636
X-RAY DIFFRACTIONf_chiral_restr0.074259
X-RAY DIFFRACTIONf_plane_restr0.004287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0001-2.12520.34771270.27232430255799
2.1252-2.28910.29661300.242456258699
2.2891-2.51910.2931290.23442455258499
2.5191-2.88260.29761290.23362450257998
2.8826-3.62820.2381290.21122455258497
3.6282-19.82490.25331330.20042516264995

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