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- PDB-3idw: Crystal structure of Sla1 homology domain 2 -

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Basic information

Entry
Database: PDB / ID: 3idw
TitleCrystal structure of Sla1 homology domain 2
ComponentsActin cytoskeleton-regulatory complex protein SLA1
KeywordsENDOCYTOSIS / clathrin adaptor / SAM domain / yeast / Actin-binding / Cell membrane / Cytoskeleton / Endosome / Membrane / Nucleus / Phosphoprotein / SH3 domain
Function / homology
Function and homology information


actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / ubiquitin binding / cell wall organization / endocytosis / actin binding / cell cortex / endosome membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Transcription Factor, Ets-1 / Variant SH3 domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Transcription Factor, Ets-1 / Variant SH3 domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / DNA polymerase; domain 1 / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Actin cytoskeleton-regulatory complex protein SLA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsDi Pietro, S.M. / Cascio, D. / Bowie, J.U. / Payne, G.S.
CitationJournal: Embo J. / Year: 2010
Title: Regulation of clathrin adaptor function in endocytosis: novel role for the SAM domain.
Authors: Di Pietro, S.M. / Cascio, D. / Feliciano, D. / Bowie, J.U. / Payne, G.S.
History
DepositionJul 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin cytoskeleton-regulatory complex protein SLA1


Theoretical massNumber of molelcules
Total (without water)8,5911
Polymers8,5911
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.273, 59.273, 47.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Actin cytoskeleton-regulatory complex protein SLA1 / Endocytic adaptor protein Sla1


Mass: 8590.744 Da / Num. of mol.: 1 / Fragment: Sla1 homology domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLA1, YBL007C, YBL0321 / Plasmid: pET-30a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: P32790
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1 M HEPES, 5% PEG-6000, 5% MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.000,0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2008 / Details: mirrors
RadiationMonochromator: Double Crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
ReflectionRedundancy: 10 % / Av σ(I) over netI: 40.81 / Number: 57070 / Rmerge(I) obs: 0.112 / Χ2: 1.18 / D res high: 2.1 Å / D res low: 80 Å / Num. obs: 5717 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.528098.510.0751.0549.9
3.594.5299.310.0820.97910.1
3.143.5999.510.0991.13310.4
2.853.1499.710.1151.20510.5
2.652.8599.510.1411.04510.4
2.492.6599.810.1891.1110.5
2.372.4999.710.250.70510.4
2.262.3799.610.3631.2489.9
2.182.2699.610.462.4959.2
2.12.1899.710.4520.9588.4
ReflectionResolution: 1.85→90 Å / Num. obs: 8256 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 18.3 % / Rmerge(I) obs: 0.061 / Χ2: 0.911 / Net I/σ(I): 41.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.9215.70.5068210.941100
1.92-1.9917.90.3668130.9491100
1.99-2.0818.60.2468041.0351100
2.08-2.1918.70.1778361.0191100
2.19-2.3318.70.1318070.9191100
2.33-2.5118.80.118310.9431100
2.51-2.7618.80.0978171.0431100
2.76-3.1618.50.0878361.1761100
3.16-3.9918.10.058360.7121100
3.99-9018.70.0338550.399199.9

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 5724
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.79-10025.10.832502
3.79-4.7920.30.936501
3.3-3.7922.10.922504
2.99-3.324.60.911503
2.78-2.9926.10.912503
2.61-2.7834.70.879509
2.47-2.6131.60.872502
2.37-2.4731.70.866503
2.27-2.3731.40.827514
2.19-2.2725.90.786504
2.1-2.1930.70.78679

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.636 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.847 / SU B: 5.688 / SU ML: 0.08 / SU R Cruickshank DPI: 0.123 / SU Rfree: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.219 375 4.6 %RANDOM
Rwork0.203 ---
obs0.204 8200 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.85 Å2 / Biso mean: 22.334 Å2 / Biso min: 13.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å20 Å2
2---0.95 Å20 Å2
3---1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.111 Å0.123 Å
Luzzati sigma a-0.08 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms551 0 0 25 576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022561
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.94752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.569565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04323.63633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65215104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.192156
X-RAY DIFFRACTIONr_chiral_restr0.0860.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02433
X-RAY DIFFRACTIONr_mcbond_it0.7641.5326
X-RAY DIFFRACTIONr_mcangle_it1.6212525
X-RAY DIFFRACTIONr_scbond_it2.9463235
X-RAY DIFFRACTIONr_scangle_it4.8354.5227
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 21 -
Rwork0.236 583 -
all-604 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -18.3904 Å / Origin y: -12.9237 Å / Origin z: 0.5489 Å
111213212223313233
T0.0113 Å2-0.0078 Å20.0147 Å2-0.0352 Å20.0173 Å2--0.0687 Å2
L3.0742 °2-0.9474 °20.2339 °2-2.9535 °20.4327 °2--3.2732 °2
S-0.0754 Å °0.1883 Å °0.0626 Å °0.0894 Å °-0.0262 Å °0.11 Å °0.111 Å °0.016 Å °0.1016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 67
2X-RAY DIFFRACTION1A73 - 97

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