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- PDB-4a5k: Structural analyses of Slm1-PH domain demonstrate ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 4a5k
TitleStructural analyses of Slm1-PH domain demonstrate ligand binding in the non-canonical site
ComponentsPHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM 1
KeywordsSIGNALING PROTEIN / NON-CANONICAL BINDING SITE / INOSITOL PHOSPHATE / PHOSPHOSERINE
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: 1.76 Å
AuthorsAnand, K. / Gavin, A.C.
CitationJournal: Plos One / Year: 2012
Title: Structural Analyses of Slm1-Ph Domain Demonstrate Ligand Binding in the Non-Canonical Site
Authors: Anand, K. / Maeda, K. / Gavin, A.C.
History
DepositionOct 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM 1
B: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM 1
C: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM 1
D: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2906
Polymers54,0984
Non-polymers1922
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.300, 82.300, 76.400
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM 1 / SLM1 / SYNTHETIC LETHAL WITH MSS4 PROTEIN 1 / TORC2 EFFECTOR PROTEIN SLM1


Mass: 13524.382 Da / Num. of mol.: 4 / Fragment: PH DOMAIN, RESIDUES 469-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: P40485
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 49444 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.2 / % possible all: 40

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NSU

3nsu


Resolution: 1.76→38.2 Å / SU ML: 0.19 / σ(F): 2.03 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1094 2.5 %
Rwork0.1883 --
obs0.1893 43738 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.861 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2745 Å20 Å2-0.7978 Å2
2---0.892 Å20 Å2
3---1.1665 Å2
Refinement stepCycle: LAST / Resolution: 1.76→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 10 356 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063785
X-RAY DIFFRACTIONf_angle_d1.0315083
X-RAY DIFFRACTIONf_dihedral_angle_d15.7151377
X-RAY DIFFRACTIONf_chiral_restr0.076550
X-RAY DIFFRACTIONf_plane_restr0.005627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.84010.26231060.19634154X-RAY DIFFRACTION75
1.8401-1.93710.24531300.1885066X-RAY DIFFRACTION91
1.9371-2.05850.26651420.19035548X-RAY DIFFRACTION99
2.0585-2.21740.21691430.18785542X-RAY DIFFRACTION100
2.2174-2.44050.21951420.18615563X-RAY DIFFRACTION100
2.4405-2.79360.23631430.19475568X-RAY DIFFRACTION100
2.7936-3.51920.24291430.18715593X-RAY DIFFRACTION100
3.5192-38.20890.20241450.18185610X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.6815 Å / Origin y: 21.8523 Å / Origin z: -18.9643 Å
111213212223313233
T0.0144 Å20.0003 Å2-0.0014 Å2-0.0307 Å2-0.0008 Å2--0.034 Å2
L0.0793 °20.0071 °2-0.0172 °2-0.1706 °2-0.0032 °2--0.1454 °2
S0.0079 Å °-0.0045 Å °0.0015 Å °-0.003 Å °-0.0134 Å °-0.04 Å °0.0002 Å °0.0144 Å °0.005 Å °
Refinement TLS groupSelection details: ALL

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