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Yorodumi- PDB-6e8m: Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e8m | ||||||
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Title | Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 pTyr381 peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Src homology 2 domain | ||||||
Function / homology | Function and homology information regulation of protein transport / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / flagellated sperm motility / C3HC4-type RING finger domain binding / Tat protein binding / negative regulation of JUN kinase activity / protein localization to mitochondrion / negative regulation of establishment of protein localization to mitochondrion / low-density lipoprotein particle receptor binding / androgen receptor signaling pathway ...regulation of protein transport / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / flagellated sperm motility / C3HC4-type RING finger domain binding / Tat protein binding / negative regulation of JUN kinase activity / protein localization to mitochondrion / negative regulation of establishment of protein localization to mitochondrion / low-density lipoprotein particle receptor binding / androgen receptor signaling pathway / ATPase activator activity / cytoplasmic side of endoplasmic reticulum membrane / response to unfolded protein / negative regulation of protein ubiquitination / Hsp70 protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / G protein-coupled receptor binding / microtubule cytoskeleton / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / protein refolding / spermatogenesis / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Legionella longbeachae serogroup 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 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 | 6e8m.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e8m.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e8m ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e8m | HTTPS FTP |
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-Related structure data
Related structure data | 6e8hSC 6e8iC 6e8kC 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: Protein/peptide | Mass: 1698.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P31689 |
#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: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / Details: PEG3000, malic acid, 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 23, 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: 1.6→33.92 Å / Num. obs: 22071 / % possible obs: 90.3 % / Redundancy: 11 % / Biso Wilson estimate: 22.21 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3192 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E8H Resolution: 1.61→24.21 Å / SU ML: 0.1863 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8337
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→24.21 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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