+Open data
-Basic information
Entry | Database: PDB / ID: 6e8i | ||||||
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Title | Legionella Longbeachae LeSH (Llo2327) bound to phosphotyrosine | ||||||
Components | LeSH (Llo2327) | ||||||
Keywords | PEPTIDE BINDING PROTEIN / Src homology 2 domain | ||||||
Function / homology | SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / O-PHOSPHOTYROSINE / SH2 domain-containing protein Function and homology information | ||||||
Biological species | Legionella longbeachae serogroup 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Kaneko, T. / Li, S.S.C. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Identification and characterization of a large family of superbinding bacterial SH2 domains. Authors: Kaneko, T. / Stogios, P.J. / Ruan, X. / Voss, C. / Evdokimova, E. / Skarina, T. / Chung, A. / Liu, X. / Li, L. / Savchenko, A. / Ensminger, A.W. / Li, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e8i.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e8i.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 6e8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e8i ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e8i | HTTPS FTP |
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-Related structure data
Related structure data | 6e8hSC 6e8kC 6e8mC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 19771.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella longbeachae serogroup 1 (strain NSW150) (bacteria) Strain: NSW150 / Gene: LLO_2327 / Production host: Escherichia coli (E. coli) / References: UniProt: D3HJY4 |
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#2: Chemical | ChemComp-PTR / |
#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: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / Details: PEG3000, sodium acetate, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 114 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→34.97 Å / Num. obs: 18762 / % possible obs: 85.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.71 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 4 / Num. unique obs: 2479 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E8H Resolution: 1.68→29.99 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.685
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→29.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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