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Yorodumi- PDB-6xnj: Crystal structure of the PDZ domain of human GOPC in complex with... -
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-Basic information
Entry | Database: PDB / ID: 6xnj | |||||||||
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Title | Crystal structure of the PDZ domain of human GOPC in complex with a peptide of E. coli O157:H7 str. Sakai effector NleG8 | |||||||||
Components |
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Keywords | PROTEIN BINDING / UBIQUITINATION / EFFECTORS / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID | |||||||||
Function / homology | Function and homology information biological process involved in symbiotic interaction / negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle ...biological process involved in symbiotic interaction / negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-protein transferase activity / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli O157:H7 str. Sakai (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Stogios, P.J. / Skarina, T. / Popov, G. / Chang, C. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: To Be Published Title: Crystal structure of the PDZ domain of human GOPC in complex with a peptide of E. coli O157:H7 str. Sakai effector NleG8 Authors: Popov, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xnj.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xnj.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xnj_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 6xnj_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 6xnj_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6xnj_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/6xnj ftp://data.pdbj.org/pub/pdb/validation_reports/xn/6xnj | HTTPS FTP |
-Related structure data
Related structure data | 4e34S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 9725.110 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q9HD26 | ||||
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#2: Protein/peptide | Mass: 1133.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 str. Sakai (bacteria) Strain: O157:H7 strain Sakai / Gene: NleG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XAN6*PLUS | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5 M ammonium sulfate, 15% sucrose, 0.1 M Hepes pH 7.5, 2 mM peptide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→35 Å / Num. obs: 14417 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Net I/σ(I): 18.11 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 723 / CC1/2: 0.967 / Rpim(I) all: 0.283 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+34 / Resolution: 1.85→34.38 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3201 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→34.38 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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