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- PDB-4a6f: Crystal structure of Slm1-PH domain in complex with Phosphoserine -

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Basic information

Entry
Database: PDB / ID: 4a6f
TitleCrystal structure of Slm1-PH domain in complex with Phosphoserine
Components(PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1) x 2
KeywordsSIGNALING PROTEIN / POST TRANSLATIONAL MODIFICATION
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
PHOSPHATE ION / PHOSPHOSERINE / Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Atomic model
Revision 1.2Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4628
Polymers27,5322
Non-polymers9306
Water3,135174
1
A: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
B: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1
hetero molecules

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)56,92516
Polymers55,0644
Non-polymers1,86012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area5880 Å2
ΔGint-64.1 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.540, 73.650, 82.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2028-

HOH

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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.: 1 / Fragment: SLM1-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 / References: UniProt: P40485
#2: Protein PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE-BINDING PROTEIN SLM1 / SYNTHETIC LETHAL WITH MSS4 PROTEIN 1 / TORC2 EFFECTOR PROTEIN SLM1


Mass: 13754.582 Da / Num. of mol.: 1 / Fragment: SLM1-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 / References: UniProt: P40485
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→20 Å / Num. obs: 26485 / % possible obs: 98.7 % / Observed criterion σ(I): 2.34 / Redundancy: 5.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.61
Reflection shellResolution: 1.68→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.34 / % possible all: 93.4

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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 4A5K

4a5k


Resolution: 1.68→54.933 Å / SU ML: 0.21 / σ(F): 2.02 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1058 4 %
Rwork0.2144 --
obs0.2155 26460 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.803 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9194 Å20 Å20 Å2
2--0.6653 Å20 Å2
3----2.5847 Å2
Refinement stepCycle: LAST / Resolution: 1.68→54.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 54 174 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061803
X-RAY DIFFRACTIONf_angle_d1.1072419
X-RAY DIFFRACTIONf_dihedral_angle_d15.504654
X-RAY DIFFRACTIONf_chiral_restr0.077268
X-RAY DIFFRACTIONf_plane_restr0.005290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6801-1.75650.27571200.23932869X-RAY DIFFRACTION91
1.7565-1.84920.29241300.22723128X-RAY DIFFRACTION99
1.8492-1.9650.24921320.21663186X-RAY DIFFRACTION100
1.965-2.11670.22751320.21173175X-RAY DIFFRACTION100
2.1167-2.32980.26221330.20863191X-RAY DIFFRACTION100
2.3298-2.66690.27751340.2243223X-RAY DIFFRACTION100
2.6669-3.35990.24121350.21823247X-RAY DIFFRACTION100
3.3599-54.96230.20821420.20193383X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.3378 Å / Origin y: -7.506 Å / Origin z: 9.3801 Å
111213212223313233
T0.0436 Å20.0015 Å20.0083 Å2--0.0022 Å20.0465 Å2--0.0315 Å2
L0.7943 °2-0.6195 °2-0.4113 °2-0.3181 °20.8465 °2--0.9037 °2
S-0.0548 Å °0.0994 Å °0.1018 Å °0.0532 Å °0.0686 Å °-0.0686 Å °0.1676 Å °-0.0673 Å °-0.0149 Å °
Refinement TLS groupSelection details: ALL

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