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Yorodumi- PDB-1ssh: Crystal structure of the SH3 domain from a S. cerevisiae hypothet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ssh | ||||||
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Title | Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein in complex with a peptide | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / SH3 domain / yeast / structural genomics / protein-peptide complex | ||||||
Function / homology | Function and homology information actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch localization / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch localization / 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 filament bundle assembly / phosphatidylinositol binding / ubiquitin binding / recycling endosome / cell wall organization / endocytosis / actin filament binding / actin binding / cell cortex / endosome membrane / mitochondrion / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Kursula, P. / Kursula, I. / Lehmann, F. / Song, Y.-H. / Wilmanns, M. | ||||||
Citation | Journal: To be Published Title: Yeast SH3 domain structural genomics Authors: Kursula, P. / Kursula, I. / Lehmann, F. / Song, Y.-H. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ssh.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ssh.ent.gz | 18.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ssh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ssh_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 1ssh_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 1ssh_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1ssh_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/1ssh ftp://data.pdbj.org/pub/pdb/validation_reports/ss/1ssh | HTTPS FTP |
-Related structure data
Related structure data | 1ootS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6581.299 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P43603 |
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#2: Protein/peptide | Mass: 1221.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic 12-aa peptide from yeast Sla1 / References: UniProt: P32790 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.9M sodium malonate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9795 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 19, 2004 |
Radiation | Monochromator: Si crystal, mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 13804 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 16.56 |
Reflection shell | Resolution: 1.4→1.5 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OOT Resolution: 1.4→18.82 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.245 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→18.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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