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- PDB-4a6h: Crystal structure of Slm1-PH domain in complex with Inositol-4- p... -

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Basic information

Entry
Database: PDB / ID: 4a6h
TitleCrystal structure of Slm1-PH domain in complex with Inositol-4- phosphate
ComponentsPHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
KeywordsSIGNALING PROTEIN
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
D-MYO-INOSITOL-4-PHOSPHATE / PHOSPHATE ION / Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsAnand, K. / Maeda, 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
DepositionNov 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2May 1, 2024Group: 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 SLM1
B: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
C: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
D: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,65115
Polymers55,1104
Non-polymers1,54011
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-85.2 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.000, 71.600, 82.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13777.617 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: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40485
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-I4D / D-MYO-INOSITOL-4-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.1 Å3/Da / Density % sol: 41.53 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0665
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0665 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 80522 / % possible obs: 99.2 % / Observed criterion σ(I): 4.01 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.01 / % possible all: 96

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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: APO STRUCTURE

Resolution: 1.449→35.808 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 1462 2 %
Rwork0.1928 --
obs0.1935 73073 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.014 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3011 Å20 Å2-0.2516 Å2
2--4.9315 Å20 Å2
3----3.6304 Å2
Refinement stepCycle: LAST / Resolution: 1.449→35.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 88 377 3965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063664
X-RAY DIFFRACTIONf_angle_d1.0144931
X-RAY DIFFRACTIONf_dihedral_angle_d17.2371367
X-RAY DIFFRACTIONf_chiral_restr0.071535
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4491-1.50080.32131400.2736840X-RAY DIFFRACTION92
1.5008-1.56090.26961430.23567003X-RAY DIFFRACTION93
1.5609-1.6320.2421440.21967063X-RAY DIFFRACTION95
1.632-1.7180.24391440.20077080X-RAY DIFFRACTION95
1.718-1.82570.20861460.19357150X-RAY DIFFRACTION96
1.8257-1.96660.231470.18397206X-RAY DIFFRACTION96
1.9666-2.16450.22371480.18427240X-RAY DIFFRACTION96
2.1645-2.47760.24531470.19237222X-RAY DIFFRACTION97
2.4776-3.12130.27581510.19887398X-RAY DIFFRACTION98
3.1213-35.81850.18071520.17857409X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 0.1406 Å / Origin y: 0.1989 Å / Origin z: 20.7521 Å
111213212223313233
T0.0373 Å20.0006 Å20.0012 Å2-0.0507 Å20.0208 Å2--0.0508 Å2
L0.164 °2-0.0005 °20.0005 °2-0.1996 °20.2791 °2--0.3884 °2
S-0.0206 Å °0.0017 Å °0.0019 Å °0.0066 Å °0.0067 Å °0.0166 Å °-0.0032 Å °0.0511 Å °0.0161 Å °
Refinement TLS groupSelection details: ALL

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